15-64891602-A-G

Variant names:

• chr15-64891602-A-G
• rs1719271
• ENST00000437723.1:c.483+30027A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

Genes affected

ENSG00000249240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437723.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249240	ENST00000437723.1	TSL:5	c.483+30027A>G		intron	N/A	ENSP00000397942.1	C9J4A7
	ENSG00000249240	ENST00000502574.1	TSL:2	n.617+30027A>G		intron	N/A

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

African (AFR) AF: 0.211 AC: 8741 AN: 41468

American (AMR) AF: 0.251 AC: 3840 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 646 AN: 3462

East Asian (EAS) AF: 0.738 AC: 3821 AN: 5180

South Asian (SAS) AF: 0.178 AC: 860 AN: 4820

European-Finnish (FIN) AF: 0.224 AC: 2364 AN: 10576

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10021 AN: 67952

Other (OTH) AF: 0.217 AC: 459 AN: 2112

Alfa AF: 0.173 Hom.: 13656

Bravo AF: 0.212

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.16

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1719271;

hg19: chr15-65183801;