rs10035961

Variant names:

• chr5-157603387-A-C
• rs10035961

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 0.389 in 152,020 control chromosomes in the GnomAD database, including 12,533 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 0.39 (12533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 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: 0.389 AC: 59133 AN: 151902 Hom.: 12515 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.389 AC: 59191 AN: 152020 Hom.: 12533 Cov.: 32 AF XY: 0.389 AC XY: 28902 AN XY: 74294

African (AFR) AF: 0.564 AC: 23352 AN: 41424

American (AMR) AF: 0.381 AC: 5822 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1367 AN: 3466

East Asian (EAS) AF: 0.128 AC: 661 AN: 5180

South Asian (SAS) AF: 0.267 AC: 1289 AN: 4824

European-Finnish (FIN) AF: 0.386 AC: 4073 AN: 10562

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21337 AN: 67952

Other (OTH) AF: 0.386 AC: 816 AN: 2112

Alfa AF: 0.340 Hom.: 26923

Bravo AF: 0.403

Asia WGS AF: 0.204 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.56
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10035961; hg19: chr5-157030395; COSMIC: COSV72872340;