12-57671665-C-T

Variant names:

• chr12-57671665-C-T
• rs2640629

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 0.587 in 151,828 control chromosomes in the GnomAD database, including 26,855 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 0.59 (26855 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89158 AN: 151708 Hom.: 26852 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.587 AC: 89191 AN: 151828 Hom.: 26855 Cov.: 31 AF XY: 0.579 AC XY: 42992 AN XY: 74212

African (AFR) AF: 0.489 AC: 20218 AN: 41346

American (AMR) AF: 0.633 AC: 9645 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2349 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1779 AN: 5148

South Asian (SAS) AF: 0.382 AC: 1840 AN: 4816

European-Finnish (FIN) AF: 0.592 AC: 6237 AN: 10538

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45131 AN: 67950

Other (OTH) AF: 0.632 AC: 1336 AN: 2114

Alfa AF: 0.534 Hom.: 2670

Bravo AF: 0.589

Asia WGS AF: 0.386 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2640629; hg19: chr12-58065448;