rs11647459

chr16-52881839-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 0.351 in 151,944 control chromosomes in the GnomAD database, including 9,889 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 0.35 (9889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 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: 0.352 AC: 53380 AN: 151826 Hom.: 9882 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.351 AC: 53405 AN: 151944 Hom.: 9889 Cov.: 32 AF XY: 0.353 AC XY: 26194 AN XY: 74206

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.357

Alfa AF: 0.379 Hom.: 1885

Bravo AF: 0.356

Asia WGS AF: 0.441 AC: 1532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.79
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11647459; hg19: chr16-52915751;