chr11-29173590-A-G

Variant names:

• chr11-29173590-A-G
• rs1491818
• ENST00000530960.1:n.184+13322A>G

Variant summary

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

The ENST00000530960.1(ENSG00000254526):​n.184+13322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,632 control chromosomes in the GnomAD database, including 6,383 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 0.28 (6383 hom., cov: 32)
• Consequence: ENSG00000254526 ENST00000530960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 4 publications found

Genes affected

ENSG00000254526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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
ENSG00000254526	ENST00000530960.1	n.184+13322A>G		intron_variant	Intron 2 of 4	3
ENSG00000254526	ENST00000742293.1	n.105+13322A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43080 AN: 151514 Hom.: 6382 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.284 AC: 43070 AN: 151632 Hom.: 6383 Cov.: 32 AF XY: 0.287 AC XY: 21233 AN XY: 74108

African (AFR) AF: 0.223 AC: 9260 AN: 41454

American (AMR) AF: 0.236 AC: 3579 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1155 AN: 3458

East Asian (EAS) AF: 0.406 AC: 2087 AN: 5142

South Asian (SAS) AF: 0.229 AC: 1103 AN: 4824

European-Finnish (FIN) AF: 0.358 AC: 3782 AN: 10558

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21082 AN: 67726

Other (OTH) AF: 0.274 AC: 580 AN: 2114

Alfa AF: 0.297 Hom.: 13375

Bravo AF: 0.273

Asia WGS AF: 0.290 AC: 1006 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Benign	0.75
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1491818; hg19: chr11-29195137;