rs11648736

Variant names:

• chr16-13957035-G-A
• rs11648736

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 0.348 in 151,852 control chromosomes in the GnomAD database, including 9,616 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 (9616 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 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: 0.348 AC: 52731 AN: 151734 Hom.: 9584 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.348 AC: 52817 AN: 151852 Hom.: 9616 Cov.: 31 AF XY: 0.343 AC XY: 25485 AN XY: 74202

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.360

Alfa AF: 0.356 Hom.: 881

Bravo AF: 0.352

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11648736; hg19: chr16-14050892;