11-121788251-T-C

Variant names:

• chr11-121788251-T-C
• rs949076
• ENST00000652518.1:n.140-81071T>C

Variant summary

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

The ENST00000652518.1(ENSG00000286044):​n.140-81071T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,156 control chromosomes in the GnomAD database, including 47,013 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 0.79 (47013 hom., cov: 32)
• Consequence: ENSG00000286044 ENST00000652518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958
• 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 = 0.899 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.140-81071T>C		intron_variant	Intron 1 of 6
ENSG00000299723	ENST00000765855.1	n.290-13693A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119449 AN: 152038 Hom.: 46971 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.786 AC: 119549 AN: 152156 Hom.: 47013 Cov.: 32 AF XY: 0.788 AC XY: 58606 AN XY: 74374

African (AFR) AF: 0.822 AC: 34153 AN: 41530

American (AMR) AF: 0.772 AC: 11806 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2694 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4774 AN: 5184

South Asian (SAS) AF: 0.774 AC: 3725 AN: 4812

European-Finnish (FIN) AF: 0.765 AC: 8106 AN: 10594

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51771 AN: 67964

Other (OTH) AF: 0.765 AC: 1615 AN: 2110

Alfa AF: 0.764 Hom.: 74389

Bravo AF: 0.789

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.42
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs949076; hg19: chr11-121658959;