ENST00000448407.1:n.100+5029G>A

Variant names:

• chr13-105500553-C-T
• rs778327
• ENST00000448407.1:n.100+5029G>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.100+5029G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,922 control chromosomes in the GnomAD database, including 29,672 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 0.61 (29672 hom., cov: 32)
• Consequence: DAOA-AS1 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAOA-AS1	NR_040247.1	n.100+5029G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAOA-AS1	ENST00000448407.1	n.100+5029G>A		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92282 AN: 151804 Hom.: 29659 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.608 AC: 92313 AN: 151922 Hom.: 29672 Cov.: 32 AF XY: 0.615 AC XY: 45681 AN XY: 74270

African (AFR) AF: 0.374 AC: 15468 AN: 41410

American (AMR) AF: 0.685 AC: 10433 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3910 AN: 5152

South Asian (SAS) AF: 0.753 AC: 3636 AN: 4826

European-Finnish (FIN) AF: 0.734 AC: 7754 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46660 AN: 67948

Other (OTH) AF: 0.616 AC: 1299 AN: 2110

Alfa AF: 0.651 Hom.: 4170

Bravo AF: 0.591

Asia WGS AF: 0.705 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.42
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs778327; hg19: chr13-106152902;