rs13138132

Variant names:

• chr4-81029366-A-C
• rs13138132

Your query was ambiguous. Multiple possible variants found:

• chr4-81029366-A-C
• chr4-81029366-A-G
• chr4-81029366-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;