12-25264360-C-T

Variant names:

• chr12-25264360-C-T
• rs4556643

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 0.542 in 151,916 control chromosomes in the GnomAD database, including 22,443 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 0.54 (22443 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 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: 0.542 AC: 82278 AN: 151798 Hom.: 22429 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.542 AC: 82317 AN: 151916 Hom.: 22443 Cov.: 31 AF XY: 0.541 AC XY: 40192 AN XY: 74242

African (AFR) AF: 0.477 AC: 19759 AN: 41396

American (AMR) AF: 0.557 AC: 8503 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1992 AN: 3472

East Asian (EAS) AF: 0.539 AC: 2783 AN: 5162

South Asian (SAS) AF: 0.588 AC: 2832 AN: 4818

European-Finnish (FIN) AF: 0.520 AC: 5488 AN: 10560

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38910 AN: 67926

Other (OTH) AF: 0.545 AC: 1150 AN: 2110

Alfa AF: 0.556 Hom.: 4805

Bravo AF: 0.539

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4556643; hg19: chr12-25417294;