13-73475711-C-T

Variant names:

• chr13-73475711-C-T
• rs10507817
• ENST00000443621.2:n.254-62075G>A

Variant summary

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

The ENST00000443621.2(LINC00393):​n.254-62075G>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 ENST00000443621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443621.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00393	ENST00000443621.2	TSL:3	n.254-62075G>A		intron	N/A
	LINC00393	ENST00000792750.1		n.240-18749G>A		intron	N/A

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

African (AFR) AF: 0.0578 AC: 2400 AN: 41510

American (AMR) AF: 0.0250 AC: 382 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.146 AC: 756 AN: 5168

South Asian (SAS) AF: 0.165 AC: 794 AN: 4814

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10578

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0153 AC: 1041 AN: 68008

Other (OTH) AF: 0.0436 AC: 92 AN: 2108

Alfa AF: 0.0269 Hom.: 15

Bravo AF: 0.0368

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		0.016
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10507817;

hg19: chr13-74049848;