rs13263637

Positions:

• chr8-18091376-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125429.1(ASAH1-AS1):​n.483+4239T>G variant causes a intron, non coding transcript 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 NR_125429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASAH1-AS1	NR_125429.1	n.483+4239T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASAH1-AS1	ENST00000665050.1	n.608+4440T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.429

Alfa AF: 0.474 Hom.: 9988

Bravo AF: 0.384

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13263637; hg19: chr8-17948885;