rs3922628

Variant names:

• chr12-122724748-T-A
• rs3922628

Your query was ambiguous. Multiple possible variants found:

• chr12-122724748-T-A
• chr12-122724748-T-C

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 0.241 in 151,028 control chromosomes in the GnomAD database, including 4,692 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 0.24 (4692 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.241 AC: 36396 AN: 150910 Hom.: 4690 Cov.: 30

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.0914

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.241 AC: 36408 AN: 151028 Hom.: 4692 Cov.: 30 AF XY: 0.238 AC XY: 17551 AN XY: 73724

African (AFR) AF: 0.298 AC: 12259 AN: 41096

American (AMR) AF: 0.201 AC: 3047 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3460

East Asian (EAS) AF: 0.497 AC: 2538 AN: 5110

South Asian (SAS) AF: 0.0919 AC: 440 AN: 4788

European-Finnish (FIN) AF: 0.216 AC: 2242 AN: 10396

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14617 AN: 67738

Other (OTH) AF: 0.217 AC: 454 AN: 2096

Alfa AF: 0.220 Hom.: 562

Bravo AF: 0.251

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.49
DANN	Benign	0.77
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3922628; hg19: chr12-123209295; COSMIC: COSV108182238;