ENST00000443621.1:n.119-52108T>C

Variant names:

• chr13-73465744-A-G
• rs10507815
• ENST00000443621.1:n.119-52108T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443621.1(LINC00393):​n.119-52108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0893 in 152,256 control chromosomes in the GnomAD database, including 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 0.089 (674 hom., cov: 32)
• Consequence: LINC00393 ENST00000443621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 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	ENST00000443621.1	n.119-52108T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13590 AN: 152140 Hom.: 674 Cov.: 32

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.0893 AC: 13600 AN: 152256 Hom.: 674 Cov.: 32 AF XY: 0.0923 AC XY: 6867 AN XY: 74436

Gnomad4 AFR AF: 0.0711

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.0904

Alfa AF: 0.0882 Hom.: 902

Bravo AF: 0.0870

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507815; hg19: chr13-74039881;