11-121927189-G-A

Variant names:

• chr11-121927189-G-A
• rs1219414
• ENST00000652518.1:n.1879-177G>A

Variant summary

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

The ENST00000652518.1(ENSG00000286044):​n.1879-177G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,028 control chromosomes in the GnomAD database, including 7,530 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 0.31 (7530 hom., cov: 32)
• Consequence: ENSG00000286044 ENST00000652518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 4 publications found

Genes affected

ENSG00000286044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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
ENSG00000286044	ENST00000652518.1	n.1879-177G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46961 AN: 151910 Hom.: 7514 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0714

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.309 AC: 46991 AN: 152028 Hom.: 7530 Cov.: 32 AF XY: 0.307 AC XY: 22779 AN XY: 74306

African (AFR) AF: 0.339 AC: 14050 AN: 41464

American (AMR) AF: 0.238 AC: 3637 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3466

East Asian (EAS) AF: 0.0710 AC: 367 AN: 5170

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4816

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10576

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22254 AN: 67950

Other (OTH) AF: 0.330 AC: 695 AN: 2106

Alfa AF: 0.324 Hom.: 25847

Bravo AF: 0.303

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.70
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1219414; hg19: chr11-121797897;