8-137893053-A-G

Variant names:

• chr8-137893053-A-G
• rs9657451
• ENST00000518973.1:n.515-55168T>C

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-55168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,058 control chromosomes in the GnomAD database, including 44,409 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 0.74 (44409 hom., cov: 31)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 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.574-55168T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253288	ENST00000518973.1	TSL:2	n.515-55168T>C		intron	N/A
	ENSG00000254361	ENST00000519652.3	TSL:4	n.315-35628A>G		intron	N/A
	ENSG00000253288	ENST00000657186.1		n.602-55168T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112220 AN: 151940 Hom.: 44385 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.739 AC: 112296 AN: 152058 Hom.: 44409 Cov.: 31 AF XY: 0.742 AC XY: 55134 AN XY: 74312

African (AFR) AF: 0.427 AC: 17706 AN: 41442

American (AMR) AF: 0.790 AC: 12087 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2846 AN: 3472

East Asian (EAS) AF: 0.868 AC: 4460 AN: 5136

South Asian (SAS) AF: 0.866 AC: 4178 AN: 4824

European-Finnish (FIN) AF: 0.886 AC: 9378 AN: 10580

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59139 AN: 68000

Other (OTH) AF: 0.744 AC: 1568 AN: 2108

Alfa AF: 0.817 Hom.: 68117

Bravo AF: 0.718

Asia WGS AF: 0.819 AC: 2850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs9657451; hg19: chr8-138905296;