rs10507815

chr13-73465744-A-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00393	ENST00000443621.1	n.119-52108T>C		intron_variant, non_coding_transcript_variant		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;