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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.821

Alfa AF: 0.839 Hom.: 14797

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4134351; hg19: chr13-83953693;