15-64891602-A-G

Position:

• chr15-64891602-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000437723.1(ENSG00000249240):​c.483+30027A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,052 control chromosomes in the GnomAD database, including 4,028 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 0.20 (4028 hom., cov: 32)
• Consequence: ENSG00000249240 ENST00000437723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

ENSG00000249240 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.64891602A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249240	ENST00000437723.1	c.483+30027A>G		intron_variant		5		ENSP00000397942.1
ENSG00000249240	ENST00000502574.1	n.617+30027A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30900 AN: 151934 Hom.: 4024 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.203 AC: 30928 AN: 152052 Hom.: 4028 Cov.: 32 AF XY: 0.209 AC XY: 15529 AN XY: 74340

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.217

Alfa AF: 0.166 Hom.: 5600

Bravo AF: 0.212

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1719271; hg19: chr15-65183801;