15-36363821-A-G

Variant names:

• chr15-36363821-A-G
• rs4459505
• ENST00000780278.1:n.65-2249T>C

Variant summary

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

The ENST00000780278.1(ENSG00000301624):​n.65-2249T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,046 control chromosomes in the GnomAD database, including 45,960 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 0.77 (45960 hom., cov: 32)
• Consequence: ENSG00000301624 ENST00000780278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 4 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=-0.89).
• 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.65-2249T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117270 AN: 151928 Hom.: 45933 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.772 AC: 117343 AN: 152046 Hom.: 45960 Cov.: 32 AF XY: 0.775 AC XY: 57569 AN XY: 74322

African (AFR) AF: 0.643 AC: 26651 AN: 41456

American (AMR) AF: 0.852 AC: 13001 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5164 AN: 5176

South Asian (SAS) AF: 0.906 AC: 4367 AN: 4822

European-Finnish (FIN) AF: 0.752 AC: 7946 AN: 10562

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54933 AN: 67982

Other (OTH) AF: 0.791 AC: 1668 AN: 2110

Alfa AF: 0.800 Hom.: 86876

Bravo AF: 0.768

Asia WGS AF: 0.936 AC: 3255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.84
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs4459505; hg19: chr15-36656022;