chr13-105458997-G-A

Variant names:

• chr13-105458997-G-A
• rs1935057
• ENST00000448407.1:n.*58C>T

Variant summary

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

The ENST00000448407.1(DAOA-AS1):​n.*58C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,360 control chromosomes in the GnomAD database, including 19,674 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 0.51 (19674 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: DAOA-AS1 ENST00000448407.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAOA-AS1	NR_040247.1	n.*58C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAOA-AS1	ENST00000448407.1	n.*58C>T		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76737 AN: 151238 Hom.: 19673 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.507 AC: 76767 AN: 151360 Hom.: 19674 Cov.: 31 AF XY: 0.504 AC XY: 37235 AN XY: 73916

African (AFR) AF: 0.436 AC: 17992 AN: 41294

American (AMR) AF: 0.518 AC: 7889 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1933 AN: 3458

East Asian (EAS) AF: 0.302 AC: 1543 AN: 5116

South Asian (SAS) AF: 0.491 AC: 2358 AN: 4798

European-Finnish (FIN) AF: 0.526 AC: 5483 AN: 10416

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37835 AN: 67748

Other (OTH) AF: 0.522 AC: 1096 AN: 2098

Alfa AF: 0.526 Hom.: 2683

Bravo AF: 0.505

Asia WGS AF: 0.422 AC: 1464 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.37
PhyloP100		-0.91
Mutation Taster		=96/4	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1935057; hg19: chr13-106111346;