rs669653

Variant names:

• chr15-47864789-G-A
• rs669653
• ENST00000662551.1:n.188+51873G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-47864789-G-A
• chr15-47864789-G-T

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+51873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,074 control chromosomes in the GnomAD database, including 2,011 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 0.12 (2011 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 2 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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
ENSG00000259754	ENST00000662551.1	n.188+51873G>A		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.188+51873G>A		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.68+51873G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18083 AN: 151956 Hom.: 1998 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.0949

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

GnomAD4 genome AF: 0.119 AC: 18152 AN: 152074 Hom.: 2011 Cov.: 32 AF XY: 0.121 AC XY: 8957 AN XY: 74330

African (AFR) AF: 0.274 AC: 11350 AN: 41426

American (AMR) AF: 0.0833 AC: 1273 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3470

East Asian (EAS) AF: 0.177 AC: 917 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4818

European-Finnish (FIN) AF: 0.0236 AC: 250 AN: 10584

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2755 AN: 68004

Other (OTH) AF: 0.101 AC: 212 AN: 2108

Alfa AF: 0.0603 Hom.: 816

Bravo AF: 0.126

Asia WGS AF: 0.245 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.48
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs669653; hg19: chr15-48156986;