13-105497692-A-T

Variant names:

• chr13-105497692-A-T
• rs778326
• ENST00000448407.1:n.101-5515T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448407.1(DAOA-AS1):​n.101-5515T>A variant causes a intron 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 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAOA-AS1	NR_040247.1		n.101-5515T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAOA-AS1	ENST00000448407.1	TSL:2	n.101-5515T>A		intron	N/A

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

African (AFR) AF: 0.217 AC: 8989 AN: 41484

American (AMR) AF: 0.267 AC: 4079 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3472

East Asian (EAS) AF: 0.135 AC: 695 AN: 5156

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4824

European-Finnish (FIN) AF: 0.329 AC: 3489 AN: 10592

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19831 AN: 67956

Other (OTH) AF: 0.249 AC: 526 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.056

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs778326;

hg19: chr13-106150041;