4-12669937-C-T

Variant names:

• chr4-12669937-C-T
• rs10516259

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 0.292 in 151,932 control chromosomes in the GnomAD database, including 7,418 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 0.29 (7418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• 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 (EAS) allele frequency at 95% confidence interval = 0.642 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: 0.292 AC: 44395 AN: 151814 Hom.: 7408 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.292 AC: 44407 AN: 151932 Hom.: 7418 Cov.: 32 AF XY: 0.303 AC XY: 22490 AN XY: 74238

African (AFR) AF: 0.176 AC: 7303 AN: 41478

American (AMR) AF: 0.389 AC: 5913 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3466

East Asian (EAS) AF: 0.661 AC: 3399 AN: 5146

South Asian (SAS) AF: 0.551 AC: 2655 AN: 4816

European-Finnish (FIN) AF: 0.332 AC: 3505 AN: 10550

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20125 AN: 67948

Other (OTH) AF: 0.287 AC: 606 AN: 2114

Alfa AF: 0.298 Hom.: 4288

Bravo AF: 0.289

Asia WGS AF: 0.557 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10516259; hg19: chr4-12671561;