rs4856346

Positions:

• chr3-81453504-T-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 0.661 in 151,836 control chromosomes in the GnomAD database, including 33,535 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 0.66 (33535 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697

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 (NFE) allele frequency at 95% confidence interval = 0.715 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: 0.661 AC: 100295 AN: 151718 Hom.: 33520 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.661 AC: 100352 AN: 151836 Hom.: 33535 Cov.: 31 AF XY: 0.657 AC XY: 48733 AN XY: 74196

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.688

Alfa AF: 0.714 Hom.: 58835

Bravo AF: 0.659

Asia WGS AF: 0.594 AC: 2067 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	0.11
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4856346; hg19: chr3-81502655;