chr13-47647608-C-T

Variant names:

• chr13-47647608-C-T
• rs1172416

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 0.711 in 151,814 control chromosomes in the GnomAD database, including 38,477 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 0.71 (38477 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 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: 0.711 AC: 107808 AN: 151696 Hom.: 38435 Cov.: 33

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.711 AC: 107902 AN: 151814 Hom.: 38477 Cov.: 33 AF XY: 0.716 AC XY: 53137 AN XY: 74206

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.690

Alfa AF: 0.699 Hom.: 16890

Bravo AF: 0.711

Asia WGS AF: 0.752 AC: 2614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1172416; hg19: chr13-48221743;