rs9318176

chr13-73422045-A-G

Variant summary

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

The ENST00000443621.1(LINC00393):n.119-8409T>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 0.0897 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 ENST00000443621.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854

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=-0.6).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00393	ENST00000443621.1	n.119-8409T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.0854

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.0725 Hom.: 62

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318176; hg19: chr13-73996182;