rs778326

chr13-105497692-A-T

Variant summary

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

The NR_040247.1(DAOA-AS1):n.101-5515T>A 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 0.262 in 152,090 control chromosomes in the GnomAD database, including 5,419 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 0.26 (5419 hom., cov: 32)
• Consequence: DAOA-AS1 NR_040247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

DAOA-AS1 (HGNC:30243): (DAOA antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAOA-AS1	NR_040247.1	n.101-5515T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAOA-AS1	ENST00000448407.1	n.101-5515T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39889 AN: 151972 Hom.: 5413 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.262 AC: 39912 AN: 152090 Hom.: 5419 Cov.: 32 AF XY: 0.261 AC XY: 19404 AN XY: 74354

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.249

Alfa AF: 0.277 Hom.: 745

Bravo AF: 0.259

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.5
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs778326; hg19: chr13-106150041;