3-13514336-C-T

Position:

• chr3-13514336-C-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 0.881 in 152,172 control chromosomes in the GnomAD database, including 59,235 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 0.88 (59235 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.881 AC: 133987 AN: 152054 Hom.: 59187 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.881 AC: 134092 AN: 152172 Hom.: 59235 Cov.: 31 AF XY: 0.883 AC XY: 65664 AN XY: 74390

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.877

Alfa AF: 0.892 Hom.: 49471

Bravo AF: 0.876

Asia WGS AF: 0.960 AC: 3340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2597513; hg19: chr3-13555836;