1-159612313-C-T

Variant names:

• chr1-159612313-C-T
• rs10494331

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 0.2 in 151,988 control chromosomes in the GnomAD database, including 3,260 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 0.20 (3260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30360 AN: 151870 Hom.: 3246 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.200 AC: 30410 AN: 151988 Hom.: 3260 Cov.: 32 AF XY: 0.204 AC XY: 15189 AN XY: 74292

African (AFR) AF: 0.185 AC: 7662 AN: 41442

American (AMR) AF: 0.188 AC: 2864 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2197 AN: 5134

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4814

European-Finnish (FIN) AF: 0.233 AC: 2457 AN: 10558

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12854 AN: 67990

Other (OTH) AF: 0.185 AC: 390 AN: 2106

Alfa AF: 0.191 Hom.: 12059

Bravo AF: 0.197

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.57
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10494331; hg19: chr1-159582103; COSMIC: COSV50656778;