12-125665095-T-G

Variant names:

• chr12-125665095-T-G
• rs2214959

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 0.689 in 152,100 control chromosomes in the GnomAD database, including 36,792 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 0.69 (36792 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.689 AC: 104748 AN: 151982 Hom.: 36770 Cov.: 33

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.689 AC: 104821 AN: 152100 Hom.: 36792 Cov.: 33 AF XY: 0.696 AC XY: 51777 AN XY: 74342

African (AFR) AF: 0.585 AC: 24264 AN: 41486

American (AMR) AF: 0.773 AC: 11820 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5153 AN: 5180

South Asian (SAS) AF: 0.736 AC: 3546 AN: 4820

European-Finnish (FIN) AF: 0.772 AC: 8155 AN: 10564

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47351 AN: 67988

Other (OTH) AF: 0.700 AC: 1468 AN: 2098

Alfa AF: 0.693 Hom.: 113720

Bravo AF: 0.690

Asia WGS AF: 0.847 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.062
DANN	Benign	0.34
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2214959; hg19: chr12-126149641;