15-79721080-T-G

Variant names:

• chr15-79721080-T-G
• rs2692194
• ENST00000756109.1:n.103+23338A>C

Variant summary

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

The ENST00000756109.1(ENSG00000298511):​n.103+23338A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 152,000 control chromosomes in the GnomAD database, including 34,475 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 0.67 (34475 hom., cov: 32)
• Consequence: ENSG00000298511 ENST00000756109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 7 publications found

Genes affected

ENSG00000298511 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756109.1. 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
	ENSG00000298511	ENST00000756109.1		n.103+23338A>C		intron	N/A
	ENSG00000298511	ENST00000756110.1		n.103+23338A>C		intron	N/A
	ENSG00000298511	ENST00000756111.1		n.95+23338A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101161 AN: 151882 Hom.: 34420 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.666 AC: 101272 AN: 152000 Hom.: 34475 Cov.: 32 AF XY: 0.658 AC XY: 48900 AN XY: 74270

African (AFR) AF: 0.786 AC: 32566 AN: 41456

American (AMR) AF: 0.706 AC: 10799 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3472

East Asian (EAS) AF: 0.515 AC: 2663 AN: 5172

South Asian (SAS) AF: 0.438 AC: 2104 AN: 4802

European-Finnish (FIN) AF: 0.558 AC: 5879 AN: 10542

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43169 AN: 67954

Other (OTH) AF: 0.670 AC: 1415 AN: 2112

Alfa AF: 0.649 Hom.: 45564

Bravo AF: 0.687

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.075
DANN	Benign	0.72
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2692194; hg19: chr15-80013422; COSMIC: COSV68084056;