ENST00000432331.3:n.483-4593T>C

Variant names:

• chr13-44111810-A-G
• rs717091
• ENST00000432331.3:n.483-4593T>C

Variant summary

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

The ENST00000432331.3(LINC00390):​n.483-4593T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,074 control chromosomes in the GnomAD database, including 37,312 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 0.66 (37312 hom., cov: 32)
• Consequence: LINC00390 ENST00000432331.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 7 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM2-AS1	NR_104065.1	n.64+1198A>G		intron_variant	Intron 1 of 4
LINC00390	NR_132368.1	n.327-4593T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00390	ENST00000432331.3	n.483-4593T>C		intron_variant	Intron 2 of 3	5
SMIM2-AS1	ENST00000618753.4	n.162+1198A>G		intron_variant	Intron 1 of 3	4
SMIM2-AS1	ENST00000619472.2	n.109+1198A>G		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100529 AN: 151956 Hom.: 37314 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.661 AC: 100531 AN: 152074 Hom.: 37312 Cov.: 32 AF XY: 0.663 AC XY: 49242 AN XY: 74320

African (AFR) AF: 0.293 AC: 12162 AN: 41466

American (AMR) AF: 0.736 AC: 11254 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3102 AN: 3470

East Asian (EAS) AF: 0.736 AC: 3796 AN: 5160

South Asian (SAS) AF: 0.653 AC: 3145 AN: 4814

European-Finnish (FIN) AF: 0.804 AC: 8501 AN: 10574

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56074 AN: 67998

Other (OTH) AF: 0.726 AC: 1527 AN: 2104

Alfa AF: 0.770 Hom.: 128869

Bravo AF: 0.642

Asia WGS AF: 0.689 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs717091; hg19: chr13-44685946;