rs3916967

Variant names:

• chr13-105464999-T-C
• rs3916967
• ENST00000448407.1:n.739+1188A>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.739+1188A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,136 control chromosomes in the GnomAD database, including 9,426 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 0.32 (9426 hom., cov: 33)
• Consequence: DAOA-AS1 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• 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 (EAS) allele frequency at 95% confidence interval = 0.612 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.739+1188A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAOA-AS1	ENST00000448407.1	TSL:2	n.739+1188A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49170 AN: 152018 Hom.: 9426 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.323 AC: 49175 AN: 152136 Hom.: 9426 Cov.: 33 AF XY: 0.331 AC XY: 24612 AN XY: 74352

African (AFR) AF: 0.115 AC: 4797 AN: 41534

American (AMR) AF: 0.392 AC: 5995 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3251 AN: 5158

South Asian (SAS) AF: 0.427 AC: 2055 AN: 4816

European-Finnish (FIN) AF: 0.438 AC: 4631 AN: 10572

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26053 AN: 67984

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.360 Hom.: 13304

Bravo AF: 0.310

Asia WGS AF: 0.463 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.2
DANN	Benign	0.89
PhyloP100		0.22

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: rs3916967;

hg19: chr13-106117348;