ENST00000443621.2:n.254-8409T>C

Variant names:

• chr13-73422045-A-G
• rs9318176
• ENST00000443621.2:n.254-8409T>C

Variant summary

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

The ENST00000443621.2(LINC00393):​n.254-8409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,226 control chromosomes in the GnomAD database, including 951 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 0.090 (951 hom., cov: 32)
• Consequence: LINC00393 ENST00000443621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854
• Publications: 0 publications found

Genes affected

LINC00393 (HGNC:42721): (long intergenic non-protein coding RNA 393)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00393	ENST00000443621.2	n.254-8409T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 13653 AN: 152108 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.0850

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0897 AC: 13662 AN: 152226 Hom.: 951 Cov.: 32 AF XY: 0.0922 AC XY: 6864 AN XY: 74446

African (AFR) AF: 0.0969 AC: 4024 AN: 41522

American (AMR) AF: 0.102 AC: 1567 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2020 AN: 5172

South Asian (SAS) AF: 0.0854 AC: 412 AN: 4822

European-Finnish (FIN) AF: 0.0730 AC: 774 AN: 10610

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4175 AN: 68014

Other (OTH) AF: 0.0855 AC: 180 AN: 2106

Alfa AF: 0.0736 Hom.: 64

Bravo AF: 0.0971

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.5
DANN	Benign	0.88
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs9318176; hg19: chr13-73996182;