13-73475711-C-T

Variant names:

• chr13-73475711-C-T
• rs10507817
• ENST00000443621.1:n.119-62075G>A

Variant summary

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

The ENST00000443621.1(LINC00393):​n.119-62075G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0388 in 152,154 control chromosomes in the GnomAD database, including 226 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 0.039 (226 hom., cov: 32)
• Consequence: LINC00393 ENST00000443621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 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.119-62075G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0388 AC: 5893 AN: 152038 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0577

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0427

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

GnomAD4 genome AF: 0.0388 AC: 5903 AN: 152154 Hom.: 226 Cov.: 32 AF XY: 0.0427 AC XY: 3177 AN XY: 74386

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.0250

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0253 Hom.: 13

Bravo AF: 0.0368

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507817; hg19: chr13-74049848;