8-18120141-C-T

Variant names:

• chr8-18120141-C-T
• rs17126232
• ENST00000659561.2:n.405-6699C>T

Variant summary

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

The ENST00000659561.2(ASAH1-AS1):​n.405-6699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,164 control chromosomes in the GnomAD database, including 884 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 0.11 (884 hom., cov: 32)
• Consequence: ASAH1-AS1 ENST00000659561.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 13 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659561.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASAH1-AS1	ENST00000659561.2		n.405-6699C>T		intron	N/A
	ASAH1-AS1	ENST00000839452.1		n.611-6699C>T		intron	N/A
	ASAH1-AS1	ENST00000839453.1		n.703-6699C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15990 AN: 152046 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.105 AC: 16019 AN: 152164 Hom.: 884 Cov.: 32 AF XY: 0.108 AC XY: 8013 AN XY: 74396

African (AFR) AF: 0.109 AC: 4544 AN: 41508

American (AMR) AF: 0.106 AC: 1627 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5172

South Asian (SAS) AF: 0.104 AC: 503 AN: 4818

European-Finnish (FIN) AF: 0.129 AC: 1365 AN: 10590

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7170 AN: 67990

Other (OTH) AF: 0.112 AC: 237 AN: 2116

Alfa AF: 0.104 Hom.: 2584

Bravo AF: 0.104

Asia WGS AF: 0.0610 AC: 211 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	0.78
DANN	Benign	0.32
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs17126232; hg19: chr8-17977650;