rs8028529

Variant names:

• chr15-36362396-C-T
• rs8028529
• ENST00000780278.1:n.65-824G>A

Variant summary

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

The ENST00000780278.1(ENSG00000301624):​n.65-824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,988 control chromosomes in the GnomAD database, including 42,741 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 0.74 (42741 hom., cov: 32)
• Consequence: ENSG00000301624 ENST00000780278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 7 publications found

Genes affected

ENSG00000301624 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000301624	ENST00000780278.1	n.65-824G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112848 AN: 151870 Hom.: 42717 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.743 AC: 112918 AN: 151988 Hom.: 42741 Cov.: 32 AF XY: 0.747 AC XY: 55508 AN XY: 74284

African (AFR) AF: 0.606 AC: 25092 AN: 41420

American (AMR) AF: 0.823 AC: 12579 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2634 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5146 AN: 5158

South Asian (SAS) AF: 0.901 AC: 4343 AN: 4822

European-Finnish (FIN) AF: 0.738 AC: 7793 AN: 10566

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.777 AC: 52823 AN: 67960

Other (OTH) AF: 0.756 AC: 1594 AN: 2108

Alfa AF: 0.768 Hom.: 151736

Bravo AF: 0.738

Asia WGS AF: 0.932 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.2
DANN	Benign	0.46
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs8028529; hg19: chr15-36654597;