4-13097258-C-T

Variant names:

• chr4-13097258-C-T
• rs512244

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 0.879 in 152,220 control chromosomes in the GnomAD database, including 58,903 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 0.88 (58903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.879 AC: 133736 AN: 152102 Hom.: 58859 Cov.: 33

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.879 AC: 133838 AN: 152220 Hom.: 58903 Cov.: 33 AF XY: 0.879 AC XY: 65415 AN XY: 74424

African (AFR) AF: 0.894 AC: 37109 AN: 41530

American (AMR) AF: 0.908 AC: 13876 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2939 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5172

South Asian (SAS) AF: 0.928 AC: 4479 AN: 4828

European-Finnish (FIN) AF: 0.816 AC: 8645 AN: 10596

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58695 AN: 68016

Other (OTH) AF: 0.884 AC: 1868 AN: 2112

Alfa AF: 0.873 Hom.: 88672

Bravo AF: 0.887

Asia WGS AF: 0.968 AC: 3364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.14
DANN	Benign	0.62
PhyloP100		-2.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs512244;

hg19: chr4-13098882;