ENST00000776537.1:n.238+15061T>A

Variant names:

• chr17-34236812-A-T
• rs9893096
• ENST00000776537.1:n.238+15061T>A

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+15061T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,114 control chromosomes in the GnomAD database, including 23,375 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 0.55 (23375 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 4 publications found

Genes affected

ENSG00000301139 (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 (AFR) allele frequency at 95% confidence interval = 0.595 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
ENSG00000301139	ENST00000776537.1	n.238+15061T>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.239-13673T>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.237-13720T>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776540.1	n.159-13720T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84107 AN: 151996 Hom.: 23362 Cov.: 33

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.553 AC: 84165 AN: 152114 Hom.: 23375 Cov.: 33 AF XY: 0.553 AC XY: 41151 AN XY: 74362

African (AFR) AF: 0.601 AC: 24952 AN: 41522

American (AMR) AF: 0.505 AC: 7718 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1820 AN: 3468

East Asian (EAS) AF: 0.441 AC: 2273 AN: 5160

South Asian (SAS) AF: 0.559 AC: 2698 AN: 4824

European-Finnish (FIN) AF: 0.554 AC: 5852 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37112 AN: 67972

Other (OTH) AF: 0.547 AC: 1154 AN: 2110

Alfa AF: 0.427 Hom.: 1168

Bravo AF: 0.553

Asia WGS AF: 0.506 AC: 1762 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	1.6
DANN	Benign	0.37
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9893096; hg19: chr17-32563831;