15-73720096-A-G

Variant names:

• chr15-73720096-A-G
• rs1038094
• ENST00000751553.1:n.644T>C

Variant summary

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

The ENST00000751553.1(ENSG00000276807):​n.644T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,196 control chromosomes in the GnomAD database, including 52,670 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 0.83 (52670 hom., cov: 33)
• Consequence: ENSG00000276807 ENST00000751553.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 17 publications found

Genes affected

ENSG00000276807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751553.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000276807	ENST00000751553.1		n.644T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125991 AN: 152076 Hom.: 52644 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.828 AC: 126073 AN: 152196 Hom.: 52670 Cov.: 33 AF XY: 0.824 AC XY: 61348 AN XY: 74430

African (AFR) AF: 0.732 AC: 30389 AN: 41490

American (AMR) AF: 0.841 AC: 12867 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3183 AN: 3472

East Asian (EAS) AF: 0.639 AC: 3303 AN: 5166

South Asian (SAS) AF: 0.750 AC: 3621 AN: 4830

European-Finnish (FIN) AF: 0.858 AC: 9085 AN: 10594

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60725 AN: 68022

Other (OTH) AF: 0.858 AC: 1813 AN: 2114

Alfa AF: 0.869 Hom.: 181735

Bravo AF: 0.823

Asia WGS AF: 0.716 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.67
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1038094; hg19: chr15-74012437;