13-105501882-C-T

Variant names:

• chr13-105501882-C-T
• rs3916970
• ENST00000448407.1:n.100+3700G>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+3700G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,206 control chromosomes in the GnomAD database, including 9,275 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 (9275 hom., cov: 30)
• Consequence: DAOA-AS1 ENST00000448407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAOA-AS1	NR_040247.1	n.100+3700G>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+3700G>A		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes AF: 0.324 AC: 48961 AN: 151090 Hom.: 9273 Cov.: 30

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.324 AC: 48962 AN: 151206 Hom.: 9275 Cov.: 30 AF XY: 0.332 AC XY: 24510 AN XY: 73770

African (AFR) AF: 0.127 AC: 5219 AN: 41136

American (AMR) AF: 0.405 AC: 6127 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1346 AN: 3460

East Asian (EAS) AF: 0.590 AC: 3027 AN: 5132

South Asian (SAS) AF: 0.537 AC: 2573 AN: 4794

European-Finnish (FIN) AF: 0.356 AC: 3722 AN: 10442

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25775 AN: 67814

Other (OTH) AF: 0.349 AC: 735 AN: 2104

Alfa AF: 0.370 Hom.: 4626

Bravo AF: 0.313

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.28
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3916970; hg19: chr13-106154231;