rs12956651

Variant names:

• chr18-72447220-A-G
• rs12956651

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 0.0772 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0432

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.0321

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.0673

Alfa AF: 0.0698 Hom.: 417

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12956651; hg19: chr18-70114455;