rs3856860

chr3-3230999-T-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 0.748 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;