rs10513577

chr3-162043443-T-C

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 0.195 in 152,172 control chromosomes in the GnomAD database, including 3,888 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 0.19 (3888 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29626 AN: 152056 Hom.: 3888 Cov.: 33

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.195 AC: 29621 AN: 152172 Hom.: 3888 Cov.: 33 AF XY: 0.192 AC XY: 14306 AN XY: 74372

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.00812

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.173

Alfa AF: 0.270 Hom.: 2926

Bravo AF: 0.171

Asia WGS AF: 0.0870 AC: 303 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.2
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513577; hg19: chr3-161761231;