rs12447924

Variant names:

• chr16-56960280-C-T
• rs12447924

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 0.757 in 152,018 control chromosomes in the GnomAD database, including 43,696 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 0.76 (43696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 33 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 = 0.773 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: 0.757 AC: 114990 AN: 151900 Hom.: 43660 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.757 AC: 115082 AN: 152018 Hom.: 43696 Cov.: 32 AF XY: 0.756 AC XY: 56197 AN XY: 74298

African (AFR) AF: 0.754 AC: 31274 AN: 41466

American (AMR) AF: 0.768 AC: 11736 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2545 AN: 3470

East Asian (EAS) AF: 0.601 AC: 3102 AN: 5158

South Asian (SAS) AF: 0.794 AC: 3826 AN: 4820

European-Finnish (FIN) AF: 0.723 AC: 7623 AN: 10544

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52357 AN: 67966

Other (OTH) AF: 0.758 AC: 1597 AN: 2106

Alfa AF: 0.763 Hom.: 20152

Bravo AF: 0.758

Asia WGS AF: 0.704 AC: 2448 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	0.13
DANN	Benign	0.32
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12447924; hg19: chr16-56994192; COSMIC: COSV52364423;