rs11661542

Variant names:

• chr18-22643732-C-A
• rs11661542
• ENST00000716263.1:n.729-30879G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000716263.1(ENSG00000266850):​n.729-30879G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000266850 ENST00000716263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 35 publications found

Genes affected

ENSG00000266850 (HGNC:58091):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266850	ENST00000716263.1	n.729-30879G>T		intron_variant	Intron 5 of 6
ENSG00000266850	ENST00000716264.1	n.924-30879G>T		intron_variant	Intron 7 of 8
ENSG00000266850	ENST00000795021.1	n.678-33539G>T		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.130 AC: 5415 AN: 41510

American (AMR) AF: 0.287 AC: 4390 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1764 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2367 AN: 5174

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4816

European-Finnish (FIN) AF: 0.579 AC: 6112 AN: 10554

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

European-Non Finnish (NFE) AF: 0.512 AC: 34779 AN: 67984

Other (OTH) AF: 0.402 AC: 848 AN: 2110

Alfa AF: 0.468 Hom.: 78254

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11661542; hg19: chr18-20223695;