rs151603

Positions:

• chr10-113970222-G-A
• chr10-113970222-G-C
• chr10-113970222-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.569 in 151,988 control chromosomes in the GnomAD database, including 25,591 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 0.57 (25591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86367 AN: 151870 Hom.: 25573 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.569 AC: 86430 AN: 151988 Hom.: 25591 Cov.: 32 AF XY: 0.578 AC XY: 42922 AN XY: 74296

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.544

Alfa AF: 0.604 Hom.: 17753

Bravo AF: 0.548

Asia WGS AF: 0.532 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs151603; hg19: chr10-115729981;