ENST00000652518.1:n.139+96683G>T

Variant names:

• chr11-121771082-G-T
• rs1944682
• ENST00000652518.1:n.139+96683G>T

Variant summary

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

The ENST00000652518.1(ENSG00000286044):​n.139+96683G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,132 control chromosomes in the GnomAD database, including 29,855 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 0.59 (29855 hom., cov: 33)
• Consequence: ENSG00000286044 ENST00000652518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913
• Publications: 3 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=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 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.139+96683G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.585 AC: 89004 AN: 152014 Hom.: 29856 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.585 AC: 89009 AN: 152132 Hom.: 29855 Cov.: 33 AF XY: 0.591 AC XY: 43996 AN XY: 74386

African (AFR) AF: 0.228 AC: 9473 AN: 41466

American (AMR) AF: 0.676 AC: 10331 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2491 AN: 3472

East Asian (EAS) AF: 0.771 AC: 3981 AN: 5164

South Asian (SAS) AF: 0.736 AC: 3550 AN: 4822

European-Finnish (FIN) AF: 0.724 AC: 7670 AN: 10596

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49370 AN: 68014

Other (OTH) AF: 0.609 AC: 1285 AN: 2110

Alfa AF: 0.651 Hom.: 4356

Bravo AF: 0.565

Asia WGS AF: 0.717 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.8
DANN	Benign	0.82
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs1944682; hg19: chr11-121641790;