rs11653011

Positions:

• chr17-55442483-T-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.55442483T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;