15-63109294-G-T

Variant names:

• chr15-63109294-G-T
• rs2729787
• ENST00000560238.1:n.371-822G>T

Variant summary

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

The ENST00000560238.1(ENSG00000259672):​n.371-822G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 151,992 control chromosomes in the GnomAD database, including 46,123 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 0.78 (46123 hom., cov: 30)
• Consequence: ENSG00000259672 ENST00000560238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 7 publications found

Genes affected

ENSG00000259672 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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
ENSG00000259672	ENST00000560238.1	n.371-822G>T		intron_variant	Intron 3 of 3	5
ENSG00000259672	ENST00000648659.1	n.693-822G>T		intron_variant	Intron 3 of 3
ENSG00000259672	ENST00000656894.1	n.326-822G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117728 AN: 151874 Hom.: 46087 Cov.: 30

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.775 AC: 117820 AN: 151992 Hom.: 46123 Cov.: 30 AF XY: 0.777 AC XY: 57722 AN XY: 74286

African (AFR) AF: 0.681 AC: 28211 AN: 41436

American (AMR) AF: 0.828 AC: 12656 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2683 AN: 3462

East Asian (EAS) AF: 0.990 AC: 5117 AN: 5170

South Asian (SAS) AF: 0.826 AC: 3977 AN: 4812

European-Finnish (FIN) AF: 0.781 AC: 8237 AN: 10546

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54384 AN: 67978

Other (OTH) AF: 0.763 AC: 1608 AN: 2108

Alfa AF: 0.778 Hom.: 6009

Bravo AF: 0.776

Asia WGS AF: 0.889 AC: 3091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.8
DANN	Benign	0.63
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2729787; hg19: chr15-63401493;