chr11-94186462-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000250519 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.408

Alfa AF: 0.220 Hom.: 475

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1540177; hg19: chr11-93919628;