rs778330

Positions:

• chr13-105502211-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_040247.1(DAOA-AS1):​n.100+3371T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.162 in 151,706 control chromosomes in the GnomAD database, including 2,255 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 (2255 hom., cov: 30)
• Consequence: DAOA-AS1 NR_040247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.79

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAOA-AS1	NR_040247.1	n.100+3371T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAOA-AS1	ENST00000448407.1	n.100+3371T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24608 AN: 151588 Hom.: 2254 Cov.: 30

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.162 AC: 24626 AN: 151706 Hom.: 2255 Cov.: 30 AF XY: 0.165 AC XY: 12222 AN XY: 74094

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.143

Alfa AF: 0.177 Hom.: 2652

Bravo AF: 0.154

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	15
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs778330; hg19: chr13-106154560;