rs1369752

Variant names:

• chr10-78488998-T-C
• rs1369752
• ENST00000421324.4:n.51-39753T>C

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.51-39753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,126 control chromosomes in the GnomAD database, including 9,155 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 0.31 (9155 hom., cov: 33)
• Consequence: ENSG00000282863 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000282863 (HGNC:):

LINC00595 (HGNC:45111): (long intergenic non-protein coding RNA 856)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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
ENSG00000282863	ENST00000421324.4	n.51-39753T>C		intron_variant	Intron 1 of 2	1
ENSG00000282863	ENST00000510550.2	n.157-36332T>C		intron_variant	Intron 1 of 3	4
LINC00595	ENST00000624665.3	n.332-36332T>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47736 AN: 152006 Hom.: 9117 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.314 AC: 47823 AN: 152126 Hom.: 9155 Cov.: 33 AF XY: 0.314 AC XY: 23355 AN XY: 74362

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.321

Alfa AF: 0.228 Hom.: 8889

Bravo AF: 0.327

Asia WGS AF: 0.380 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369752; hg19: chr10-80248755;