ENST00000448407.1:n.100+6077G>A

Variant names:

• chr13-105499505-C-T
• rs954580
• ENST00000448407.1:n.100+6077G>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+6077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,908 control chromosomes in the GnomAD database, including 29,734 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 (29734 hom., cov: 32)
• Consequence: DAOA-AS1 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 6 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 (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+6077G>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+6077G>A		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92434 AN: 151790 Hom.: 29722 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.609 AC: 92465 AN: 151908 Hom.: 29734 Cov.: 32 AF XY: 0.616 AC XY: 45737 AN XY: 74262

African (AFR) AF: 0.377 AC: 15628 AN: 41420

American (AMR) AF: 0.684 AC: 10427 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2329 AN: 3468

East Asian (EAS) AF: 0.759 AC: 3923 AN: 5170

South Asian (SAS) AF: 0.754 AC: 3633 AN: 4818

European-Finnish (FIN) AF: 0.733 AC: 7756 AN: 10576

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

European-Non Finnish (NFE) AF: 0.687 AC: 46644 AN: 67904

Other (OTH) AF: 0.618 AC: 1302 AN: 2108

Alfa AF: 0.662 Hom.: 150357

Bravo AF: 0.592

Asia WGS AF: 0.702 AC: 2441 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.61
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs954580; hg19: chr13-106151854;