4-81029366-A-C

Variant names:

• chr4-81029366-A-C
• rs13138132

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 0.669 in 152,178 control chromosomes in the GnomAD database, including 38,775 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 0.67 (38775 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101786 AN: 152060 Hom.: 38757 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.669 AC: 101816 AN: 152178 Hom.: 38775 Cov.: 33 AF XY: 0.671 AC XY: 49959 AN XY: 74422

African (AFR) AF: 0.272 AC: 11282 AN: 41498

American (AMR) AF: 0.775 AC: 11851 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2364 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4178 AN: 5172

South Asian (SAS) AF: 0.819 AC: 3956 AN: 4828

European-Finnish (FIN) AF: 0.793 AC: 8389 AN: 10582

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57374 AN: 68012

Other (OTH) AF: 0.690 AC: 1459 AN: 2116

Alfa AF: 0.677 Hom.: 5915

Bravo AF: 0.648

Asia WGS AF: 0.770 AC: 2678 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.078
DANN	Benign	0.82
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs13138132; hg19: chr4-81950520;