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 ENST00000832857.1(ENSG00000253374):​n.327-8595T>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 ENST00000832857.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253374	ENST00000524085.2	TSL:5	n.435-8595T>C		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.327-8595T>C		intron	N/A
	ENSG00000253374	ENST00000832858.1		n.309-8595T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1486004;

hg19: chr8-82425347;