rs13322435

chr3-157077679-A-G

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 0.465 in 152,048 control chromosomes in the GnomAD database, including 16,924 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 0.47 (16924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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: 0.465 AC: 70700 AN: 151930 Hom.: 16903 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.465 AC: 70759 AN: 152048 Hom.: 16924 Cov.: 32 AF XY: 0.464 AC XY: 34460 AN XY: 74324

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.494

Alfa AF: 0.446 Hom.: 1930

Bravo AF: 0.478

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.5
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13322435; hg19: chr3-156795468;