ENST00000814126.1:n.136-1143C>A

Variant names:

• chr11-116827022-C-A
• rs2542051
• ENST00000814126.1:n.136-1143C>A

Variant summary

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

The ENST00000814126.1(ENSG00000305923):​n.136-1143C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,142 control chromosomes in the GnomAD database, including 22,499 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 0.53 (22499 hom., cov: 33)
• Consequence: ENSG00000305923 ENST00000814126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 9 publications found

Genes affected

ENSG00000305923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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
ENSG00000305923	ENST00000814126.1	n.136-1143C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80076 AN: 152024 Hom.: 22501 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.526 AC: 80096 AN: 152142 Hom.: 22499 Cov.: 33 AF XY: 0.521 AC XY: 38788 AN XY: 74384

African (AFR) AF: 0.315 AC: 13077 AN: 41490

American (AMR) AF: 0.566 AC: 8655 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3170 AN: 5168

South Asian (SAS) AF: 0.488 AC: 2356 AN: 4828

European-Finnish (FIN) AF: 0.587 AC: 6220 AN: 10600

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42769 AN: 67972

Other (OTH) AF: 0.548 AC: 1158 AN: 2112

Alfa AF: 0.589 Hom.: 41011

Bravo AF: 0.525

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.022
DANN	Benign	0.78
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2542051; hg19: chr11-116697738;