15-78404150-A-G

Variant names:

• chr15-78404150-A-G
• rs6495296
• ENST00000760515.1:n.230-2395A>G

Variant summary

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

The ENST00000760515.1(ENSG00000299108):​n.230-2395A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,154 control chromosomes in the GnomAD database, including 36,291 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 0.68 (36291 hom., cov: 33)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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.230-2395A>G		intron_variant	Intron 2 of 2
ENSG00000299108	ENST00000760516.1	n.238-2395A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103751 AN: 152038 Hom.: 36233 Cov.: 33

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.683 AC: 103869 AN: 152154 Hom.: 36291 Cov.: 33 AF XY: 0.686 AC XY: 51062 AN XY: 74384

African (AFR) AF: 0.832 AC: 34549 AN: 41518

American (AMR) AF: 0.714 AC: 10919 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2136 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3857 AN: 5178

South Asian (SAS) AF: 0.690 AC: 3323 AN: 4818

European-Finnish (FIN) AF: 0.651 AC: 6894 AN: 10586

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39928 AN: 67978

Other (OTH) AF: 0.677 AC: 1428 AN: 2110

Alfa AF: 0.609 Hom.: 18684

Bravo AF: 0.694

Asia WGS AF: 0.754 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.43
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs6495296; hg19: chr15-78696492;