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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: 1-161119909-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=161119909&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 161119909,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_005600.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.548C>G",
"hgvs_p": "p.Pro183Arg",
"transcript": "NM_005600.3",
"protein_id": "NP_005591.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 327,
"cds_start": 548,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000368009.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005600.3"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.548C>G",
"hgvs_p": "p.Pro183Arg",
"transcript": "ENST00000368009.7",
"protein_id": "ENSP00000356988.2",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 327,
"cds_start": 548,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005600.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368009.7"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.548C>G",
"hgvs_p": "p.Pro183Arg",
"transcript": "ENST00000368008.5",
"protein_id": "ENSP00000356987.1",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 243,
"cds_start": 548,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368008.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "n.1112C>G",
"hgvs_p": null,
"transcript": "ENST00000496861.5",
"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": "ENST00000496861.5"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.542C>G",
"hgvs_p": "p.Pro181Arg",
"transcript": "ENST00000865251.1",
"protein_id": "ENSP00000535310.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 325,
"cds_start": 542,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865251.1"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.539C>G",
"hgvs_p": "p.Pro180Arg",
"transcript": "ENST00000935621.1",
"protein_id": "ENSP00000605680.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 324,
"cds_start": 539,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935621.1"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.503C>G",
"hgvs_p": "p.Pro168Arg",
"transcript": "NM_001185093.2",
"protein_id": "NP_001172022.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 312,
"cds_start": 503,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001185093.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.503C>G",
"hgvs_p": "p.Pro168Arg",
"transcript": "ENST00000368007.8",
"protein_id": "ENSP00000356986.4",
"transcript_support_level": 2,
"aa_start": 168,
"aa_end": null,
"aa_length": 312,
"cds_start": 503,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368007.8"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.440C>G",
"hgvs_p": "p.Pro147Arg",
"transcript": "NM_001185094.2",
"protein_id": "NP_001172023.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 291,
"cds_start": 440,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001185094.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.440C>G",
"hgvs_p": "p.Pro147Arg",
"transcript": "ENST00000392190.9",
"protein_id": "ENSP00000376028.5",
"transcript_support_level": 3,
"aa_start": 147,
"aa_end": null,
"aa_length": 291,
"cds_start": 440,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392190.9"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.407C>G",
"hgvs_p": "p.Pro136Arg",
"transcript": "ENST00000940923.1",
"protein_id": "ENSP00000610982.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 280,
"cds_start": 407,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940923.1"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.548C>G",
"hgvs_p": "p.Pro183Arg",
"transcript": "NM_001185092.2",
"protein_id": "NP_001172021.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 243,
"cds_start": 548,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001185092.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.197C>G",
"hgvs_p": "p.Pro66Arg",
"transcript": "ENST00000935622.1",
"protein_id": "ENSP00000605681.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 210,
"cds_start": 197,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935622.1"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.599C>G",
"hgvs_p": "p.Pro200Arg",
"transcript": "XM_005245214.3",
"protein_id": "XP_005245271.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 344,
"cds_start": 599,
"cds_end": null,
"cds_length": 1035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245214.3"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.599C>G",
"hgvs_p": "p.Pro200Arg",
"transcript": "XM_005245215.6",
"protein_id": "XP_005245272.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 344,
"cds_start": 599,
"cds_end": null,
"cds_length": 1035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245215.6"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.440C>G",
"hgvs_p": "p.Pro147Arg",
"transcript": "XM_005245216.5",
"protein_id": "XP_005245273.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 291,
"cds_start": 440,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245216.5"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.599C>G",
"hgvs_p": "p.Pro200Arg",
"transcript": "XM_024447363.2",
"protein_id": "XP_024303131.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 260,
"cds_start": 599,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024447363.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.599C>G",
"hgvs_p": "p.Pro200Arg",
"transcript": "XM_047421417.1",
"protein_id": "XP_047277373.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 260,
"cds_start": 599,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421417.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "c.99-10C>G",
"hgvs_p": null,
"transcript": "ENST00000865250.1",
"protein_id": "ENSP00000535309.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 174,
"cds_start": null,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865250.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "n.676C>G",
"hgvs_p": null,
"transcript": "ENST00000461376.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000461376.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "n.524C>G",
"hgvs_p": null,
"transcript": "ENST00000479266.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000479266.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIT1",
"gene_hgnc_id": 7828,
"hgvs_c": "n.562C>G",
"hgvs_p": null,
"transcript": "ENST00000485594.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000485594.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
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{
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"canonical": false,
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"strand": true,
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],
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{
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"strand": true,
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{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
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"exon_count": 4,
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"gene_symbol": "NIT1",
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"biotype": "pseudogene",
"feature": "ENST00000477684.5"
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],
"gene_symbol": "NIT1",
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"dbsnp": "rs1315826766",
"frequency_reference_population": 0.000006571684,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657168,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6222139596939087,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.492,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1389,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.688,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005600.3",
"gene_symbol": "NIT1",
"hgnc_id": 7828,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.548C>G",
"hgvs_p": "p.Pro183Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}