ENST00000524425.1:n.465-9645G>A

Variant names:

• chr8-53206654-G-A
• rs1425902
• ENST00000524425.1:n.465-9645G>A

Variant summary

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

The ENST00000524425.1(ENSG00000254687):​n.465-9645G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,088 control chromosomes in the GnomAD database, including 25,498 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 0.54 (25498 hom., cov: 32)
• Consequence: ENSG00000254687 ENST00000524425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 10 publications found

Genes affected

ENSG00000254687 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375836	NR_188096.1	n.434-9645G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254687	ENST00000524425.1	n.465-9645G>A		intron_variant	Intron 1 of 2	3
ENSG00000254687	ENST00000529837.1	n.434-9645G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82743 AN: 151970 Hom.: 25499 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.544 AC: 82757 AN: 152088 Hom.: 25498 Cov.: 32 AF XY: 0.545 AC XY: 40532 AN XY: 74358

African (AFR) AF: 0.234 AC: 9711 AN: 41484

American (AMR) AF: 0.601 AC: 9185 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3597 AN: 5160

South Asian (SAS) AF: 0.546 AC: 2629 AN: 4818

European-Finnish (FIN) AF: 0.691 AC: 7311 AN: 10578

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46319 AN: 67982

Other (OTH) AF: 0.567 AC: 1196 AN: 2110

Alfa AF: 0.645 Hom.: 50568

Bravo AF: 0.527

Asia WGS AF: 0.593 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.80
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1425902; hg19: chr8-54119214;