15-63104668-A-G

Variant names:

• chr15-63104668-A-G
• rs2652834
• ENST00000560238.1:n.112-417A>G

Variant summary

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

The ENST00000560238.1(ENSG00000259672):​n.112-417A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 151,954 control chromosomes in the GnomAD database, including 46,572 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 (46572 hom., cov: 30)
• Consequence: ENSG00000259672 ENST00000560238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54
• Publications: 74 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560238.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259672	ENST00000560238.1	TSL:5	n.112-417A>G		intron	N/A
	ENSG00000259672	ENST00000648659.1		n.434-417A>G		intron	N/A
	ENSG00000259672	ENST00000656894.1		n.3-417A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118394 AN: 151836 Hom.: 46537 Cov.: 30

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.780 AC: 118488 AN: 151954 Hom.: 46572 Cov.: 30 AF XY: 0.781 AC XY: 58042 AN XY: 74282

African (AFR) AF: 0.695 AC: 28764 AN: 41392

American (AMR) AF: 0.829 AC: 12661 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2701 AN: 3468

East Asian (EAS) AF: 0.989 AC: 5120 AN: 5176

South Asian (SAS) AF: 0.826 AC: 3979 AN: 4816

European-Finnish (FIN) AF: 0.782 AC: 8249 AN: 10544

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54448 AN: 67978

Other (OTH) AF: 0.768 AC: 1618 AN: 2108

Alfa AF: 0.797 Hom.: 138798

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.24
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs2652834; hg19: chr15-63396867;