rs872212

Variant names:

• chr3-148668960-A-G
• rs872212

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.724 in 152,138 control chromosomes in the GnomAD database, including 41,255 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 0.72 (41255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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: 0.724 AC: 110083 AN: 152020 Hom.: 41223 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.724 AC: 110165 AN: 152138 Hom.: 41255 Cov.: 32 AF XY: 0.728 AC XY: 54196 AN XY: 74396

African (AFR) AF: 0.522 AC: 21634 AN: 41464

American (AMR) AF: 0.824 AC: 12602 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2889 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4803 AN: 5174

South Asian (SAS) AF: 0.668 AC: 3230 AN: 4832

European-Finnish (FIN) AF: 0.821 AC: 8699 AN: 10594

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53828 AN: 67998

Other (OTH) AF: 0.738 AC: 1561 AN: 2114

Alfa AF: 0.742 Hom.: 7460

Bravo AF: 0.720

Asia WGS AF: 0.770 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.70
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs872212; hg19: chr3-148386747;