chr8-18091376-T-G

Variant names:

• chr8-18091376-T-G
• rs13263637
• ENST00000499554.6:n.483+4239T>G

Variant summary

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

The ENST00000499554.6(ASAH1-AS1):​n.483+4239T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,996 control chromosomes in the GnomAD database, including 13,952 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 0.40 (13952 hom., cov: 32)
• Consequence: ASAH1-AS1 ENST00000499554.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 4 publications found

Genes affected

ASAH1-AS1 (HGNC:55603): (ASAH1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499554.6. 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
	ASAH1-AS1	NR_125429.1		n.483+4239T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASAH1-AS1	ENST00000499554.6	TSL:3	n.483+4239T>G		intron	N/A
	ASAH1-AS1	ENST00000521775.6	TSL:4	n.1129+4440T>G		intron	N/A
	ASAH1-AS1	ENST00000649327.1		n.549+4440T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60426 AN: 151878 Hom.: 13954 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.398 AC: 60423 AN: 151996 Hom.: 13952 Cov.: 32 AF XY: 0.397 AC XY: 29484 AN XY: 74302

African (AFR) AF: 0.155 AC: 6410 AN: 41440

American (AMR) AF: 0.427 AC: 6520 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1457 AN: 3460

East Asian (EAS) AF: 0.373 AC: 1930 AN: 5168

South Asian (SAS) AF: 0.416 AC: 2007 AN: 4824

European-Finnish (FIN) AF: 0.504 AC: 5323 AN: 10562

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35339 AN: 67972

Other (OTH) AF: 0.429 AC: 907 AN: 2112

Alfa AF: 0.474 Hom.: 13429

Bravo AF: 0.384

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.74
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs13263637; hg19: chr8-17948885;