rs1603810

Variant names:

• chr12-63522902-G-A
• rs1603810

Your query was ambiguous. Multiple possible variants found:

• chr12-63522902-G-A
• chr12-63522902-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.299 in 151,890 control chromosomes in the GnomAD database, including 8,996 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (8996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45334 AN: 151772 Hom.: 8951 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.261

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.299 AC: 45435 AN: 151890 Hom.: 8996 Cov.: 32 AF XY: 0.295 AC XY: 21865 AN XY: 74188

African (AFR) AF: 0.561 AC: 23245 AN: 41408

American (AMR) AF: 0.289 AC: 4409 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5164

South Asian (SAS) AF: 0.118 AC: 569 AN: 4806

European-Finnish (FIN) AF: 0.194 AC: 2046 AN: 10536

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12273 AN: 67940

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.220 Hom.: 14530

Bravo AF: 0.320

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1603810; hg19: chr12-63916682;