ENST00000518973.1:n.515-59591A>G

Variant names:

• chr8-137897476-T-C
• rs62531686
• ENST00000518973.1:n.515-59591A>G

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-59591A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,814 control chromosomes in the GnomAD database, including 26,619 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 0.57 (26619 hom., cov: 30)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC401478	NR_161374.1	n.574-59591A>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253288	ENST00000518973.1	n.515-59591A>G		intron_variant	Intron 1 of 2	2
ENSG00000254361	ENST00000519652.3	n.315-31205T>C		intron_variant	Intron 2 of 2	4
ENSG00000253288	ENST00000657186.1	n.602-59591A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85805 AN: 151696 Hom.: 26611 Cov.: 30

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.566 AC: 85853 AN: 151814 Hom.: 26619 Cov.: 30 AF XY: 0.573 AC XY: 42474 AN XY: 74162

African (AFR) AF: 0.293 AC: 12135 AN: 41370

American (AMR) AF: 0.630 AC: 9607 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2000 AN: 3464

East Asian (EAS) AF: 0.850 AC: 4377 AN: 5150

South Asian (SAS) AF: 0.751 AC: 3615 AN: 4814

European-Finnish (FIN) AF: 0.696 AC: 7328 AN: 10530

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44976 AN: 67934

Other (OTH) AF: 0.549 AC: 1157 AN: 2108

Alfa AF: 0.506 Hom.: 8311

Bravo AF: 0.549

Asia WGS AF: 0.747 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.79
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs62531686; hg19: chr8-138909719;