ENST00000526041.2:n.283+15103C>T

Variant names:

• chr11-109022640-G-A
• rs7101378
• ENST00000526041.2:n.283+15103C>T

Variant summary

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

The ENST00000526041.2(ENSG00000255528):​n.283+15103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,854 control chromosomes in the GnomAD database, including 11,755 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 (11755 hom., cov: 31)
• Consequence: ENSG00000255528 ENST00000526041.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 4 publications found

Genes affected

ENSG00000255528 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 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
ENSG00000255528	ENST00000526041.2	n.283+15103C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58442 AN: 151736 Hom.: 11758 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.385 AC: 58451 AN: 151854 Hom.: 11755 Cov.: 31 AF XY: 0.378 AC XY: 28049 AN XY: 74192

African (AFR) AF: 0.280 AC: 11605 AN: 41442

American (AMR) AF: 0.395 AC: 6028 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1749 AN: 3460

East Asian (EAS) AF: 0.248 AC: 1279 AN: 5152

South Asian (SAS) AF: 0.376 AC: 1804 AN: 4804

European-Finnish (FIN) AF: 0.332 AC: 3488 AN: 10502

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31019 AN: 67924

Other (OTH) AF: 0.394 AC: 832 AN: 2112

Alfa AF: 0.435 Hom.: 41316

Bravo AF: 0.384

Asia WGS AF: 0.350 AC: 1218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.71
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs7101378; hg19: chr11-108893367;