rs954581

chr13-105499917-T-C

Variant summary

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

The NR_040247.1(DAOA-AS1):n.100+5665A>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 0.158 in 151,904 control chromosomes in the GnomAD database, including 1,968 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 0.16 (1968 hom., cov: 32)
• Consequence: DAOA-AS1 NR_040247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAOA-AS1	NR_040247.1	n.100+5665A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAOA-AS1	ENST00000448407.1	n.100+5665A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23945 AN: 151786 Hom.: 1966 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.158 AC: 23957 AN: 151904 Hom.: 1968 Cov.: 32 AF XY: 0.153 AC XY: 11394 AN XY: 74258

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0386

Gnomad4 SAS AF: 0.0767

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.156

Alfa AF: 0.158 Hom.: 247

Bravo AF: 0.163

Asia WGS AF: 0.0740 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.5
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs954581; hg19: chr13-106152266;