rs10494656

Variant names:

• chr1-191666689-T-C
• rs10494656

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 0.0493 in 152,132 control chromosomes in the GnomAD database, including 344 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 0.049 (344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7478 AN: 152014 Hom.: 341 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0493 AC: 7504 AN: 152132 Hom.: 344 Cov.: 32 AF XY: 0.0487 AC XY: 3624 AN XY: 74388

African (AFR) AF: 0.125 AC: 5187 AN: 41492

American (AMR) AF: 0.0284 AC: 433 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3470

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5174

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4826

European-Finnish (FIN) AF: 0.0195 AC: 207 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1229 AN: 67988

Other (OTH) AF: 0.0431 AC: 91 AN: 2112

Alfa AF: 0.0293 Hom.: 67

Bravo AF: 0.0531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.39
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10494656; hg19: chr1-191635819; COSMIC: COSV69614259;