15-78389734-C-T

Variant names:

• chr15-78389734-C-T
• rs4243082
• ENST00000760515.1:n.77-1527C>T

Variant summary

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

The ENST00000760515.1(ENSG00000299108):​n.77-1527C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,190 control chromosomes in the GnomAD database, including 44,754 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 0.76 (44754 hom., cov: 33)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 5 publications found

Genes affected

ENSG00000299108 (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 (AFR) allele frequency at 95% confidence interval = 0.893 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
ENSG00000299108	ENST00000760515.1	n.77-1527C>T		intron_variant	Intron 1 of 2
ENSG00000299108	ENST00000760516.1	n.85-1527C>T		intron_variant	Intron 1 of 4
ENSG00000299108	ENST00000760517.1	n.70-1527C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115708 AN: 152072 Hom.: 44686 Cov.: 33

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.761 AC: 115838 AN: 152190 Hom.: 44754 Cov.: 33 AF XY: 0.763 AC XY: 56775 AN XY: 74394

African (AFR) AF: 0.901 AC: 37429 AN: 41540

American (AMR) AF: 0.776 AC: 11873 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2460 AN: 3470

East Asian (EAS) AF: 0.837 AC: 4329 AN: 5170

South Asian (SAS) AF: 0.720 AC: 3471 AN: 4820

European-Finnish (FIN) AF: 0.707 AC: 7487 AN: 10590

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46346 AN: 67990

Other (OTH) AF: 0.747 AC: 1579 AN: 2114

Alfa AF: 0.706 Hom.: 76180

Bravo AF: 0.774

Asia WGS AF: 0.811 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4243082; hg19: chr15-78682076;