rs1172416

chr13-47647608-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 0.711 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;