rs1486004

Variant names:

• chr8-81513112-T-C
• rs1486004
• ENST00000524085.2:n.435-8595T>C

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.435-8595T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,996 control chromosomes in the GnomAD database, including 16,598 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 0.42 (16598 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 2 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.518-12731T>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.435-8595T>C		intron_variant	Intron 3 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-8595T>C		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-8595T>C		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-8595T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64323 AN: 151878 Hom.: 16549 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.424 AC: 64437 AN: 151996 Hom.: 16598 Cov.: 32 AF XY: 0.420 AC XY: 31197 AN XY: 74290

African (AFR) AF: 0.727 AC: 30123 AN: 41448

American (AMR) AF: 0.421 AC: 6416 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.129 AC: 667 AN: 5182

South Asian (SAS) AF: 0.383 AC: 1850 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2975 AN: 10552

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20290 AN: 67962

Other (OTH) AF: 0.409 AC: 862 AN: 2108

Alfa AF: 0.320 Hom.: 9407

Bravo AF: 0.446

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.82
DANN	Benign	0.67
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1486004; hg19: chr8-82425347;