ENST00000763069.1:n.128+7600G>T

Variant names:

• chr15-35054340-C-A
• rs10162694
• ENST00000763069.1:n.128+7600G>T

Variant summary

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

The ENST00000763069.1(ENSG00000289289):​n.128+7600G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 152,178 control chromosomes in the GnomAD database, including 209 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 0.034 (209 hom., cov: 32)
• Consequence: ENSG00000289289 ENST00000763069.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 4 publications found

Genes affected

ENSG00000289289 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763069.1. 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
	ENSG00000289289	ENST00000763069.1		n.128+7600G>T		intron	N/A
	ENSG00000289289	ENST00000763070.1		n.125-5964G>T		intron	N/A
	ENSG00000289289	ENST00000763071.1		n.127+7600G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0337 AC: 5117 AN: 152060 Hom.: 206 Cov.: 32

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00132

Gnomad OTH AF: 0.0310

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

GnomAD4 genome AF: 0.0337 AC: 5133 AN: 152178 Hom.: 209 Cov.: 32 AF XY: 0.0352 AC XY: 2618 AN XY: 74396

African (AFR) AF: 0.0688 AC: 2853 AN: 41498

American (AMR) AF: 0.0999 AC: 1525 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.113 AC: 582 AN: 5168

South Asian (SAS) AF: 0.00310 AC: 15 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00132 AC: 90 AN: 68018

Other (OTH) AF: 0.0307 AC: 65 AN: 2116

Alfa AF: 0.0204 Hom.: 277

Bravo AF: 0.0444

Asia WGS AF: 0.0410 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs10162694; hg19: chr15-35346541;