chr13-105502211-A-G

Variant names:

• chr13-105502211-A-G
• rs778330
• ENST00000448407.1:n.100+3371T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000448407.1(DAOA-AS1):​n.100+3371T>C variant causes a intron 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 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.79
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448407.1. 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
	DAOA-AS1	NR_040247.1		n.100+3371T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAOA-AS1	ENST00000448407.1	TSL:2	n.100+3371T>C		intron	N/A

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

African (AFR) AF: 0.0897 AC: 3713 AN: 41406

American (AMR) AF: 0.149 AC: 2265 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3466

East Asian (EAS) AF: 0.197 AC: 1016 AN: 5160

South Asian (SAS) AF: 0.206 AC: 990 AN: 4800

European-Finnish (FIN) AF: 0.243 AC: 2552 AN: 10506

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13097 AN: 67890

Other (OTH) AF: 0.143 AC: 302 AN: 2108

Alfa AF: 0.175 Hom.: 3691

Bravo AF: 0.154

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	15
DANN	Benign	0.64
PhyloP100		4.8

Splicing

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

Other links and lift over

dbSNP: rs778330; hg19: chr13-106154560;