rs13322435

Variant names:

• chr3-157077679-A-G
• rs13322435

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;