rs13138132

chr4-81029366-A-Cchr4-81029366-A-Gchr4-81029366-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.690

Alfa AF: 0.693 Hom.: 5880

Bravo AF: 0.648

Asia WGS AF: 0.770 AC: 2678 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.078
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13138132; hg19: chr4-81950520;