15-72978107-C-T

Variant names:

• chr15-72978107-C-T
• rs6495038
• ENST00000760339.1:n.*39C>T

Variant summary

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

The ENST00000760339.1(ENSG00000299079):​n.*39C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,468 control chromosomes in the GnomAD database, including 28,456 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 0.61 (28456 hom., cov: 31)
• Consequence: ENSG00000299079 ENST00000760339.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 1 publications found

Genes affected

ENSG00000299079 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000760339.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299079	ENST00000760339.1		n.*39C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92502 AN: 151352 Hom.: 28430 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.611 AC: 92566 AN: 151468 Hom.: 28456 Cov.: 31 AF XY: 0.611 AC XY: 45169 AN XY: 73974

African (AFR) AF: 0.572 AC: 23600 AN: 41232

American (AMR) AF: 0.576 AC: 8786 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2137 AN: 3464

East Asian (EAS) AF: 0.516 AC: 2642 AN: 5122

South Asian (SAS) AF: 0.594 AC: 2860 AN: 4814

European-Finnish (FIN) AF: 0.696 AC: 7292 AN: 10480

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.637 AC: 43189 AN: 67804

Other (OTH) AF: 0.638 AC: 1347 AN: 2110

Alfa AF: 0.627 Hom.: 3831

Bravo AF: 0.603

Asia WGS AF: 0.536 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.084

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6495038;

hg19: chr15-73270448;