chr11-121787804-A-G

Variant names:

• chr11-121787804-A-G
• rs952151
• ENST00000652518.1:n.140-81518A>G

Variant summary

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

The ENST00000652518.1(ENSG00000286044):​n.140-81518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,126 control chromosomes in the GnomAD database, including 34,655 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 0.65 (34655 hom., cov: 33)
• Consequence: ENSG00000286044 ENST00000652518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652518.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286044	ENST00000652518.1		n.140-81518A>G		intron	N/A
	ENSG00000299723	ENST00000765855.1		n.290-13246T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99037 AN: 152008 Hom.: 34647 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.651 AC: 99079 AN: 152126 Hom.: 34655 Cov.: 33 AF XY: 0.657 AC XY: 48892 AN XY: 74386

African (AFR) AF: 0.368 AC: 15242 AN: 41472

American (AMR) AF: 0.715 AC: 10931 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2630 AN: 3470

East Asian (EAS) AF: 0.872 AC: 4513 AN: 5176

South Asian (SAS) AF: 0.770 AC: 3714 AN: 4822

European-Finnish (FIN) AF: 0.765 AC: 8100 AN: 10590

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51645 AN: 67990

Other (OTH) AF: 0.671 AC: 1413 AN: 2106

Alfa AF: 0.621 Hom.: 4368

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.54
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs952151; hg19: chr11-121658512;