11-94186462-C-T

Variant names:

• chr11-94186462-C-T
• rs1540177
• ENST00000655054.1:n.143+881C>T

Variant summary

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

The ENST00000655054.1(ENSG00000250519):​n.143+881C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,022 control chromosomes in the GnomAD database, including 10,737 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 0.37 (10737 hom., cov: 32)
• Consequence: ENSG00000250519 ENST00000655054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 4 publications found

Genes affected

ENSG00000250519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 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
ENSG00000250519	ENST00000655054.1	n.143+881C>T		intron_variant	Intron 1 of 2
ENSG00000250519	ENST00000733069.1	n.314+528C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56177 AN: 151904 Hom.: 10719 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.370 AC: 56226 AN: 152022 Hom.: 10737 Cov.: 32 AF XY: 0.370 AC XY: 27459 AN XY: 74306

African (AFR) AF: 0.290 AC: 12036 AN: 41458

American (AMR) AF: 0.450 AC: 6881 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1407 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2260 AN: 5162

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4812

European-Finnish (FIN) AF: 0.389 AC: 4105 AN: 10562

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27070 AN: 67962

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.225 Hom.: 511

Bravo AF: 0.378

Asia WGS AF: 0.363 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.22
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1540177; hg19: chr11-93919628;