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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-58660038-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=58660038&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 58660038,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001085487.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2446G>A",
"hgvs_p": "p.Gly816Arg",
"transcript": "NM_001085487.3",
"protein_id": "NP_001078956.1",
"transcript_support_level": null,
"aa_start": 816,
"aa_end": null,
"aa_length": 828,
"cds_start": 2446,
"cds_end": null,
"cds_length": 2487,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000472487.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001085487.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2446G>A",
"hgvs_p": "p.Gly816Arg",
"transcript": "ENST00000472487.6",
"protein_id": "ENSP00000418734.1",
"transcript_support_level": 1,
"aa_start": 816,
"aa_end": null,
"aa_length": 828,
"cds_start": 2446,
"cds_end": null,
"cds_length": 2487,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001085487.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000472487.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.2291G>A",
"hgvs_p": null,
"transcript": "ENST00000401044.7",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000401044.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.2495G>A",
"hgvs_p": null,
"transcript": "ENST00000493821.6",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000493821.6"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2443G>A",
"hgvs_p": "p.Gly815Arg",
"transcript": "ENST00000930864.1",
"protein_id": "ENSP00000600923.1",
"transcript_support_level": null,
"aa_start": 815,
"aa_end": null,
"aa_length": 827,
"cds_start": 2443,
"cds_end": null,
"cds_length": 2484,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930864.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2422G>A",
"hgvs_p": "p.Gly808Arg",
"transcript": "ENST00000697255.1",
"protein_id": "ENSP00000513212.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 820,
"cds_start": 2422,
"cds_end": null,
"cds_length": 2463,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000697255.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2443G>A",
"hgvs_p": "p.Gly815Arg",
"transcript": "XM_006710314.4",
"protein_id": "XP_006710377.1",
"transcript_support_level": null,
"aa_start": 815,
"aa_end": null,
"aa_length": 827,
"cds_start": 2443,
"cds_end": null,
"cds_length": 2484,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006710314.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2245G>A",
"hgvs_p": "p.Gly749Arg",
"transcript": "XM_011540573.4",
"protein_id": "XP_011538875.1",
"transcript_support_level": null,
"aa_start": 749,
"aa_end": null,
"aa_length": 761,
"cds_start": 2245,
"cds_end": null,
"cds_length": 2286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540573.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2179G>A",
"hgvs_p": "p.Gly727Arg",
"transcript": "XM_011540574.3",
"protein_id": "XP_011538876.1",
"transcript_support_level": null,
"aa_start": 727,
"aa_end": null,
"aa_length": 739,
"cds_start": 2179,
"cds_end": null,
"cds_length": 2220,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540574.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.1687G>A",
"hgvs_p": "p.Gly563Arg",
"transcript": "XM_047443717.1",
"protein_id": "XP_047299673.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 575,
"cds_start": 1687,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443717.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.1687G>A",
"hgvs_p": "p.Gly563Arg",
"transcript": "XM_047443718.1",
"protein_id": "XP_047299674.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 575,
"cds_start": 1687,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443718.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.1687G>A",
"hgvs_p": "p.Gly563Arg",
"transcript": "XM_047443719.1",
"protein_id": "XP_047299675.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 575,
"cds_start": 1687,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443719.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "c.2328+1132G>A",
"hgvs_p": null,
"transcript": "ENST00000655340.1",
"protein_id": "ENSP00000499373.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 806,
"cds_start": null,
"cds_end": null,
"cds_length": 2421,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000655340.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.*4104G>A",
"hgvs_p": null,
"transcript": "ENST00000659108.1",
"protein_id": "ENSP00000499571.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000659108.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.*935G>A",
"hgvs_p": null,
"transcript": "ENST00000659812.2",
"protein_id": "ENSP00000499686.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000659812.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.2481G>A",
"hgvs_p": null,
"transcript": "ENST00000660611.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000660611.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.*810G>A",
"hgvs_p": null,
"transcript": "ENST00000665648.1",
"protein_id": "ENSP00000499586.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000665648.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.2069G>A",
"hgvs_p": null,
"transcript": "ENST00000697250.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000697250.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.987G>A",
"hgvs_p": null,
"transcript": "ENST00000697251.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000697251.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.1564G>A",
"hgvs_p": null,
"transcript": "ENST00000697252.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000697252.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.*2038G>A",
"hgvs_p": null,
"transcript": "ENST00000697253.1",
"protein_id": "ENSP00000513210.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000697253.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"hgvs_c": "n.*2093G>A",
"hgvs_p": null,
"transcript": "ENST00000697254.1",
"protein_id": "ENSP00000513211.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000697254.1"
},
{
"aa_ref": null,
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{
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{
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"consequences": [
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"feature": "ENST00000697258.1"
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{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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{
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"exon_count": 20,
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"gene_symbol": "MYSM1",
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"hgvs_c": "n.*935G>A",
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"transcript": "ENST00000659812.2",
"protein_id": "ENSP00000499686.2",
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{
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{
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],
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"transcript": "ENST00000697253.1",
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{
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"feature": "ENST00000697254.1"
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{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
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"feature": "ENST00000637377.2"
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{
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"intron_variant"
],
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"biotype": "pseudogene",
"feature": "ENST00000767021.1"
},
{
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"strand": true,
"consequences": [
"intron_variant"
],
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"gene_symbol": "ENSG00000283445",
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"transcript": "ENST00000767022.1",
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"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000767022.1"
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],
"gene_symbol": "MYSM1",
"gene_hgnc_id": 29401,
"dbsnp": "rs201900540",
"frequency_reference_population": 0.000007464534,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000480983,
"gnomad_genomes_af": 0.0000328407,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10118919610977173,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.064,
"revel_prediction": "Benign",
"alphamissense_score": 0.0833,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.463,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001085487.3",
"gene_symbol": "MYSM1",
"hgnc_id": 29401,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2446G>A",
"hgvs_p": "p.Gly816Arg"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000767021.1",
"gene_symbol": "ENSG00000283445",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.189-54794C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}