rs3013646

Variant names:

• chr13-84747321-T-G
• rs3013646

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 0.4 in 152,030 control chromosomes in the GnomAD database, including 13,380 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 0.40 (13380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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: 0.400 AC: 60789 AN: 151910 Hom.: 13380 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.400 AC: 60792 AN: 152030 Hom.: 13380 Cov.: 32 AF XY: 0.394 AC XY: 29256 AN XY: 74332

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.410

Alfa AF: 0.446 Hom.: 2343

Bravo AF: 0.385

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3013646; hg19: chr13-85321456;