13-73429887-C-T

Variant names:

• chr13-73429887-C-T
• rs9573193
• ENST00000443621.2:n.254-16251G>A

Variant summary

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

The ENST00000443621.2(LINC00393):​n.254-16251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,050 control chromosomes in the GnomAD database, including 6,879 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 0.29 (6879 hom., cov: 32)
• Consequence: LINC00393 ENST00000443621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 5 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=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 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.254-16251G>A		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43307 AN: 151932 Hom.: 6864 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.285 AC: 43376 AN: 152050 Hom.: 6879 Cov.: 32 AF XY: 0.287 AC XY: 21335 AN XY: 74306

African (AFR) AF: 0.362 AC: 15027 AN: 41470

American (AMR) AF: 0.252 AC: 3855 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3470

East Asian (EAS) AF: 0.620 AC: 3198 AN: 5158

South Asian (SAS) AF: 0.359 AC: 1728 AN: 4814

European-Finnish (FIN) AF: 0.212 AC: 2242 AN: 10566

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15336 AN: 67978

Other (OTH) AF: 0.274 AC: 580 AN: 2114

Alfa AF: 0.241 Hom.: 2237

Bravo AF: 0.294

Asia WGS AF: 0.465 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.48
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs9573193; hg19: chr13-74004024;