rs10494132

Variant names:

• chr1-111289601-T-C
• rs10494132

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 0.258 in 152,156 control chromosomes in the GnomAD database, including 5,455 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 0.26 (5455 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.258 AC: 39218 AN: 152038 Hom.: 5455 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.258 AC: 39240 AN: 152156 Hom.: 5455 Cov.: 33 AF XY: 0.257 AC XY: 19149 AN XY: 74398

African (AFR) AF: 0.347 AC: 14379 AN: 41494

American (AMR) AF: 0.185 AC: 2825 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3470

East Asian (EAS) AF: 0.0906 AC: 468 AN: 5166

South Asian (SAS) AF: 0.240 AC: 1158 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2869 AN: 10590

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15872 AN: 68006

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.250 Hom.: 5073

Bravo AF: 0.253

Asia WGS AF: 0.171 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs10494132; hg19: chr1-111832223;