rs11647459

Variant names:

• chr16-52881839-C-T
• rs11647459

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.229 AC: 9504 AN: 41448

American (AMR) AF: 0.440 AC: 6706 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3470

East Asian (EAS) AF: 0.598 AC: 3083 AN: 5154

South Asian (SAS) AF: 0.405 AC: 1950 AN: 4816

European-Finnish (FIN) AF: 0.402 AC: 4238 AN: 10534

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25587 AN: 67972

Other (OTH) AF: 0.357 AC: 755 AN: 2114

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11647459; hg19: chr16-52915751;