rs11661542

chr18-22643732-C-A

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 0.384 in 152,108 control chromosomes in the GnomAD database, including 13,509 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 0.38 (13509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58366 AN: 151990 Hom.: 13510 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.384 AC: 58364 AN: 152108 Hom.: 13509 Cov.: 32 AF XY: 0.385 AC XY: 28632 AN XY: 74362

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.402

Alfa AF: 0.489 Hom.: 39770

Bravo AF: 0.352

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.31
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11661542; hg19: chr18-20223695;