12-25691931-C-T

Variant names:

• chr12-25691931-C-T
• rs4963910

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 0.095 in 151,696 control chromosomes in the GnomAD database, including 791 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 0.095 (791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.0951 AC: 14415 AN: 151580 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0950 AC: 14412 AN: 151696 Hom.: 791 Cov.: 32 AF XY: 0.0963 AC XY: 7132 AN XY: 74090

African (AFR) AF: 0.0558 AC: 2303 AN: 41296

American (AMR) AF: 0.0756 AC: 1153 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3468

East Asian (EAS) AF: 0.0165 AC: 85 AN: 5156

South Asian (SAS) AF: 0.0973 AC: 467 AN: 4800

European-Finnish (FIN) AF: 0.142 AC: 1482 AN: 10438

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7716 AN: 67968

Other (OTH) AF: 0.107 AC: 225 AN: 2108

Alfa AF: 0.105 Hom.: 2947

Bravo AF: 0.0864

Asia WGS AF: 0.0510 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.65
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4963910; hg19: chr12-25844865;