rs11653011

Variant names:

• chr17-55442483-T-C
• rs11653011

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 0.388 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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

African (AFR) AF: 0.320 AC: 13256 AN: 41382

American (AMR) AF: 0.446 AC: 6800 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1676 AN: 5166

South Asian (SAS) AF: 0.239 AC: 1148 AN: 4804

European-Finnish (FIN) AF: 0.382 AC: 4024 AN: 10538

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29406 AN: 67914

Other (OTH) AF: 0.381 AC: 805 AN: 2114

Alfa AF: 0.415 Hom.: 44277

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
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs11653011; hg19: chr17-53519844;