rs12956651

Variant names:

• chr18-72447220-A-G
• rs12956651

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 0.0772 in 149,342 control chromosomes in the GnomAD database, including 488 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 0.077 (488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0772 AC: 11521 AN: 149226 Hom.: 485 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0348

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0772 AC: 11532 AN: 149342 Hom.: 488 Cov.: 32 AF XY: 0.0761 AC XY: 5538 AN XY: 72742

African (AFR) AF: 0.104 AC: 4319 AN: 41422

American (AMR) AF: 0.0432 AC: 626 AN: 14474

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 298 AN: 3444

East Asian (EAS) AF: 0.0321 AC: 163 AN: 5082

South Asian (SAS) AF: 0.119 AC: 554 AN: 4668

European-Finnish (FIN) AF: 0.0546 AC: 556 AN: 10174

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0721 AC: 4818 AN: 66842

Other (OTH) AF: 0.0673 AC: 138 AN: 2052

Alfa AF: 0.0716 Hom.: 615

Bravo AF: 0.0751

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.57
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs12956651; hg19: chr18-70114455;