rs4134351

Variant names:

• chr13-83379558-A-C
• rs4134351

Your query was ambiguous. Multiple possible variants found:

• chr13-83379558-A-C
• chr13-83379558-A-G
• chr13-83379558-A-T

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 0.805 in 151,834 control chromosomes in the GnomAD database, including 49,957 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 0.81 (49957 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.864 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: 0.805 AC: 122166 AN: 151716 Hom.: 49913 Cov.: 30

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.805 AC: 122271 AN: 151834 Hom.: 49957 Cov.: 30 AF XY: 0.802 AC XY: 59514 AN XY: 74176

African (AFR) AF: 0.755 AC: 31258 AN: 41414

American (AMR) AF: 0.877 AC: 13379 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2940 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2034 AN: 5134

South Asian (SAS) AF: 0.845 AC: 4061 AN: 4804

European-Finnish (FIN) AF: 0.799 AC: 8395 AN: 10510

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57369 AN: 67928

Other (OTH) AF: 0.821 AC: 1733 AN: 2110

Alfa AF: 0.840 Hom.: 17514

Bravo AF: 0.805

Asia WGS AF: 0.678 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.46
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4134351; hg19: chr13-83953693;