15-78384471-G-C

Variant names:

• chr15-78384471-G-C
• rs4243079
• ENST00000760515.1:n.77-6790G>C

Variant summary

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

The ENST00000760515.1(ENSG00000299108):​n.77-6790G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,184 control chromosomes in the GnomAD database, including 53,818 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 0.84 (53818 hom., cov: 32)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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.77-6790G>C		intron_variant	Intron 1 of 2
ENSG00000299108	ENST00000760516.1	n.85-6790G>C		intron_variant	Intron 1 of 4
ENSG00000299108	ENST00000760517.1	n.70-6790G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127627 AN: 152066 Hom.: 53758 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.839 AC: 127748 AN: 152184 Hom.: 53818 Cov.: 32 AF XY: 0.841 AC XY: 62547 AN XY: 74372

African (AFR) AF: 0.922 AC: 38276 AN: 41536

American (AMR) AF: 0.850 AC: 12994 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2965 AN: 3472

East Asian (EAS) AF: 0.924 AC: 4778 AN: 5170

South Asian (SAS) AF: 0.796 AC: 3836 AN: 4818

European-Finnish (FIN) AF: 0.833 AC: 8817 AN: 10584

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53339 AN: 67994

Other (OTH) AF: 0.831 AC: 1754 AN: 2110

Alfa AF: 0.771 Hom.: 2199

Bravo AF: 0.854

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4243079; hg19: chr15-78676813;