chr13-105463160-T-C

Variant names:

• chr13-105463160-T-C
• rs1341402
• ENST00000448407.1:n.740-653A>G

Variant summary

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

The ENST00000448407.1(DAOA-AS1):​n.740-653A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,170 control chromosomes in the GnomAD database, including 2,508 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 (2508 hom., cov: 33)
• Consequence: DAOA-AS1 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 14 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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.740-653A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAOA-AS1	ENST00000448407.1	TSL:2	n.740-653A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23910 AN: 152052 Hom.: 2508 Cov.: 33

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0717

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.157 AC: 23914 AN: 152170 Hom.: 2508 Cov.: 33 AF XY: 0.154 AC XY: 11462 AN XY: 74392

African (AFR) AF: 0.0378 AC: 1573 AN: 41568

American (AMR) AF: 0.141 AC: 2151 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3464

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5174

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4824

European-Finnish (FIN) AF: 0.242 AC: 2563 AN: 10570

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15792 AN: 67976

Other (OTH) AF: 0.163 AC: 345 AN: 2116

Alfa AF: 0.139 Hom.: 813

Bravo AF: 0.145

Asia WGS AF: 0.0390 AC: 138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.4
DANN	Benign	0.77
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1341402; hg19: chr13-106115509;