ENST00000769376.1:n.121-24735G>A

Variant names:

• chr15-55109840-G-A
• rs10444801
• ENST00000769376.1:n.121-24735G>A

Variant summary

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

The ENST00000769376.1(ENSG00000260937):​n.121-24735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 151,990 control chromosomes in the GnomAD database, including 46,366 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 0.77 (46366 hom., cov: 30)
• Consequence: ENSG00000260937 ENST00000769376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 1 publications found

Genes affected

ENSG00000260937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 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
ENSG00000260937	ENST00000769376.1	n.121-24735G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117150 AN: 151870 Hom.: 46357 Cov.: 30

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.771 AC: 117201 AN: 151990 Hom.: 46366 Cov.: 30 AF XY: 0.776 AC XY: 57625 AN XY: 74292

African (AFR) AF: 0.577 AC: 23873 AN: 41406

American (AMR) AF: 0.864 AC: 13204 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2997 AN: 3472

East Asian (EAS) AF: 0.875 AC: 4511 AN: 5156

South Asian (SAS) AF: 0.834 AC: 4008 AN: 4804

European-Finnish (FIN) AF: 0.835 AC: 8827 AN: 10570

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57249 AN: 67994

Other (OTH) AF: 0.803 AC: 1690 AN: 2104

Alfa AF: 0.808 Hom.: 21072

Bravo AF: 0.764

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.40
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs10444801; hg19: chr15-55402038;