13-44128733-T-A

Variant names:

• chr13-44128733-T-A
• rs9525916
• ENST00000432331.3:n.482+8370A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000432331.3(LINC00390):​n.482+8370A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,970 control chromosomes in the GnomAD database, including 16,208 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 0.42 (16208 hom., cov: 31)
• Consequence: LINC00390 ENST00000432331.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05
• Publications: 10 publications found

Genes affected

LINC00390 (HGNC:42718): (long intergenic non-protein coding RNA 390)

SMIM2-AS1 (HGNC:42674): (SMIM2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM2-AS1	NR_104065.1	n.65-14824T>A		intron_variant	Intron 1 of 4
LINC00390	NR_132368.1	n.326+8370A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00390	ENST00000432331.3	n.482+8370A>T		intron_variant	Intron 2 of 3	5
SMIM2-AS1	ENST00000618753.4	n.163-18049T>A		intron_variant	Intron 1 of 3	4
SMIM2-AS1	ENST00000619472.2	n.110-14824T>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63711 AN: 151852 Hom.: 16210 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.419 AC: 63692 AN: 151970 Hom.: 16208 Cov.: 31 AF XY: 0.416 AC XY: 30909 AN XY: 74258

African (AFR) AF: 0.135 AC: 5597 AN: 41486

American (AMR) AF: 0.480 AC: 7330 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2056 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1076 AN: 5166

South Asian (SAS) AF: 0.391 AC: 1880 AN: 4808

European-Finnish (FIN) AF: 0.523 AC: 5516 AN: 10538

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38627 AN: 67918

Other (OTH) AF: 0.460 AC: 971 AN: 2112

Alfa AF: 0.493 Hom.: 2509

Bravo AF: 0.404

Asia WGS AF: 0.290 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.90
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs9525916; hg19: chr13-44702869;