rs11653011

Variant names:

• chr17-55442483-T-C
• rs11653011

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 0.388 in 151,854 control chromosomes in the GnomAD database, including 11,682 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 0.39 (11682 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 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: 0.388 AC: 58841 AN: 151734 Hom.: 11657 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.388 AC: 58911 AN: 151854 Hom.: 11682 Cov.: 32 AF XY: 0.384 AC XY: 28500 AN XY: 74222

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.381

Alfa AF: 0.421 Hom.: 28205

Bravo AF: 0.394

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11653011; hg19: chr17-53519844;