rs11640993

Variant names:

• chr16-52852693-G-A
• rs11640993

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 0.373 in 152,070 control chromosomes in the GnomAD database, including 10,861 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 0.37 (10861 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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: 0.373 AC: 56639 AN: 151952 Hom.: 10853 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.373 AC: 56663 AN: 152070 Hom.: 10861 Cov.: 33 AF XY: 0.373 AC XY: 27755 AN XY: 74356

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.377

Alfa AF: 0.390 Hom.: 11350

Bravo AF: 0.381

Asia WGS AF: 0.451 AC: 1567 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11640993; hg19: chr16-52886605;