rs342758

Positions:

• chr3-32513688-A-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 0.574 in 151,980 control chromosomes in the GnomAD database, including 25,714 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 (25714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.574 AC: 87189 AN: 151862 Hom.: 25682 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.574 AC: 87272 AN: 151980 Hom.: 25714 Cov.: 32 AF XY: 0.565 AC XY: 42004 AN XY: 74288

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.585

Alfa AF: 0.549 Hom.: 9706

Bravo AF: 0.591

Asia WGS AF: 0.468 AC: 1622 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342758; hg19: chr3-32555180;