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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: 1-48298889-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=48298889&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 48298889,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_019073.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1291T>A",
"hgvs_p": "p.Cys431Ser",
"transcript": "NM_019073.4",
"protein_id": "NP_061946.1",
"transcript_support_level": null,
"aa_start": 431,
"aa_end": null,
"aa_length": 488,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371847.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019073.4"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1291T>A",
"hgvs_p": "p.Cys431Ser",
"transcript": "ENST00000371847.8",
"protein_id": "ENSP00000360913.3",
"transcript_support_level": 1,
"aa_start": 431,
"aa_end": null,
"aa_length": 488,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_019073.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371847.8"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1243T>A",
"hgvs_p": "p.Cys415Ser",
"transcript": "ENST00000371843.7",
"protein_id": "ENSP00000360909.3",
"transcript_support_level": 1,
"aa_start": 415,
"aa_end": null,
"aa_length": 472,
"cds_start": 1243,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371843.7"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1249T>A",
"hgvs_p": "p.Cys417Ser",
"transcript": "NM_001286239.2",
"protein_id": "NP_001273168.1",
"transcript_support_level": null,
"aa_start": 417,
"aa_end": null,
"aa_length": 474,
"cds_start": 1249,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286239.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1249T>A",
"hgvs_p": "p.Cys417Ser",
"transcript": "ENST00000396199.7",
"protein_id": "ENSP00000379502.4",
"transcript_support_level": 2,
"aa_start": 417,
"aa_end": null,
"aa_length": 474,
"cds_start": 1249,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396199.7"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1243T>A",
"hgvs_p": "p.Cys415Ser",
"transcript": "NM_001286238.2",
"protein_id": "NP_001273167.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 472,
"cds_start": 1243,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286238.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1210T>A",
"hgvs_p": "p.Cys404Ser",
"transcript": "ENST00000872886.1",
"protein_id": "ENSP00000542945.1",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 461,
"cds_start": 1210,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872886.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1201T>A",
"hgvs_p": "p.Cys401Ser",
"transcript": "ENST00000872888.1",
"protein_id": "ENSP00000542947.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 458,
"cds_start": 1201,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872888.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1162T>A",
"hgvs_p": "p.Cys388Ser",
"transcript": "ENST00000872885.1",
"protein_id": "ENSP00000542944.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 445,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872885.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1075T>A",
"hgvs_p": "p.Cys359Ser",
"transcript": "ENST00000930128.1",
"protein_id": "ENSP00000600187.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 416,
"cds_start": 1075,
"cds_end": null,
"cds_length": 1251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930128.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1006T>A",
"hgvs_p": "p.Cys336Ser",
"transcript": "ENST00000872887.1",
"protein_id": "ENSP00000542946.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 393,
"cds_start": 1006,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872887.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.790T>A",
"hgvs_p": "p.Cys264Ser",
"transcript": "ENST00000930129.1",
"protein_id": "ENSP00000600188.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 321,
"cds_start": 790,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930129.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.502T>A",
"hgvs_p": "p.Cys168Ser",
"transcript": "ENST00000930127.1",
"protein_id": "ENSP00000600186.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 225,
"cds_start": 502,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930127.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1075T>A",
"hgvs_p": "p.Cys359Ser",
"transcript": "XM_017001510.2",
"protein_id": "XP_016856999.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 416,
"cds_start": 1075,
"cds_end": null,
"cds_length": 1251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001510.2"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1199T>A",
"hgvs_p": "p.Met400Lys",
"transcript": "XM_017001511.3",
"protein_id": "XP_016857000.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 410,
"cds_start": 1199,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001511.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1027T>A",
"hgvs_p": "p.Cys343Ser",
"transcript": "XM_047422902.1",
"protein_id": "XP_047278858.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 400,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047422902.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.1006T>A",
"hgvs_p": "p.Cys336Ser",
"transcript": "XM_011541606.3",
"protein_id": "XP_011539908.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 393,
"cds_start": 1006,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541606.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.979T>A",
"hgvs_p": "p.Cys327Ser",
"transcript": "XM_011541607.3",
"protein_id": "XP_011539909.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 384,
"cds_start": 979,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541607.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.967T>A",
"hgvs_p": "p.Cys323Ser",
"transcript": "XM_011541609.3",
"protein_id": "XP_011539911.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 380,
"cds_start": 967,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541609.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.967T>A",
"hgvs_p": "p.Cys323Ser",
"transcript": "XM_017001513.2",
"protein_id": "XP_016857002.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 380,
"cds_start": 967,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001513.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.967T>A",
"hgvs_p": "p.Cys323Ser",
"transcript": "XM_047422904.1",
"protein_id": "XP_047278860.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 380,
"cds_start": 967,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047422904.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"hgvs_c": "c.925T>A",
"hgvs_p": "p.Cys309Ser",
"transcript": "XM_047422906.1",
"protein_id": "XP_047278862.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 366,
"cds_start": 925,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
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{
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{
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{
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},
{
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},
{
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"feature": "XM_047422901.1"
},
{
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],
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"transcript": "XM_047422913.1",
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{
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],
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"gene_symbol": "SPATA6",
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"protein_id": "ENSP00000474844.1",
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"biotype": "nonsense_mediated_decay",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
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"exon_count": 9,
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"gene_symbol": "SPATA6",
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000603831.5"
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],
"gene_symbol": "SPATA6",
"gene_hgnc_id": 18309,
"dbsnp": "rs748620425",
"frequency_reference_population": 0.000002054392,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205439,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.018747806549072266,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.036,
"revel_prediction": "Benign",
"alphamissense_score": 0.0874,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.634,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_019073.4",
"gene_symbol": "SPATA6",
"hgnc_id": 18309,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1291T>A",
"hgvs_p": "p.Cys431Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}