rs10507815

Variant names:

• chr13-73465744-A-G
• rs10507815
• ENST00000443621.2:n.254-52108T>C

Variant summary

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

The ENST00000443621.2(LINC00393):​n.254-52108T>C variant causes a intron 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 ENST00000443621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 1 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=-0.81).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00393	ENST00000443621.2	n.254-52108T>C		intron_variant	Intron 3 of 3	3
LINC00393	ENST00000792750.1	n.240-8782T>C		intron_variant	Intron 3 of 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

African (AFR) AF: 0.0711 AC: 2955 AN: 41552

American (AMR) AF: 0.0822 AC: 1258 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3466

East Asian (EAS) AF: 0.171 AC: 884 AN: 5170

South Asian (SAS) AF: 0.172 AC: 831 AN: 4824

European-Finnish (FIN) AF: 0.103 AC: 1088 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0887 AC: 6030 AN: 68020

Other (OTH) AF: 0.0904 AC: 191 AN: 2112

Alfa AF: 0.0884 Hom.: 1325

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
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10507815; hg19: chr13-74039881;