ENST00000518973.1:n.515-18564A>G

Variant names:

• chr8-137856449-T-C
• rs7003495
• ENST00000518973.1:n.515-18564A>G

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-18564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,126 control chromosomes in the GnomAD database, including 2,685 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 0.18 (2685 hom., cov: 32)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 1 publications found

Genes affected

ENSG00000253288 (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 (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518973.1. 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
	LOC401478	NR_161374.1		n.574-18564A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253288	ENST00000518973.1	TSL:2	n.515-18564A>G		intron	N/A
	ENSG00000254361	ENST00000519652.3	TSL:4	n.252-608T>C		intron	N/A
	ENSG00000253288	ENST00000657186.1		n.602-18564A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27413 AN: 152008 Hom.: 2677 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.180 AC: 27447 AN: 152126 Hom.: 2685 Cov.: 32 AF XY: 0.177 AC XY: 13192 AN XY: 74368

African (AFR) AF: 0.120 AC: 4970 AN: 41506

American (AMR) AF: 0.178 AC: 2716 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3470

East Asian (EAS) AF: 0.0556 AC: 288 AN: 5176

South Asian (SAS) AF: 0.123 AC: 592 AN: 4814

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10580

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15281 AN: 67986

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.213 Hom.: 1912

Bravo AF: 0.175

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs7003495; hg19: chr8-138868692;