rs3856860

Variant names:

• chr3-3230999-T-C
• rs3856860

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 0.748 in 152,012 control chromosomes in the GnomAD database, including 42,792 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 0.75 (42792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.777 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: 0.749 AC: 113730 AN: 151894 Hom.: 42783 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.748 AC: 113780 AN: 152012 Hom.: 42792 Cov.: 32 AF XY: 0.748 AC XY: 55575 AN XY: 74276

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.737

Alfa AF: 0.778 Hom.: 5752

Bravo AF: 0.737

Asia WGS AF: 0.694 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3856860; hg19: chr3-3272683;