rs10504435

Variant names:

• chr8-68988668-T-C
• rs10504435
• ENST00000518540.5:n.416-34506A>G

Variant summary

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

The ENST00000518540.5(LINC01592):​n.416-34506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0584 in 152,244 control chromosomes in the GnomAD database, including 442 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 0.058 (442 hom., cov: 31)
• Consequence: LINC01592 ENST00000518540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 0 publications found

Genes affected

LINC01592 (HGNC:51557): (long intergenic non-protein coding RNA 1592)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01592	NR_039986.1	n.416-34506A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01592	ENST00000518540.5	n.416-34506A>G		intron_variant	Intron 2 of 4	2
LINC01592	ENST00000519062.7	n.149+12716A>G		intron_variant	Intron 1 of 3	3
LINC01592	ENST00000524286.2	n.166+9636A>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0583 AC: 8871 AN: 152126 Hom.: 442 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.00762

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0584 AC: 8885 AN: 152244 Hom.: 442 Cov.: 31 AF XY: 0.0590 AC XY: 4389 AN XY: 74448

African (AFR) AF: 0.116 AC: 4801 AN: 41518

American (AMR) AF: 0.0864 AC: 1321 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0210 AC: 73 AN: 3470

East Asian (EAS) AF: 0.129 AC: 666 AN: 5176

South Asian (SAS) AF: 0.0989 AC: 477 AN: 4824

European-Finnish (FIN) AF: 0.00762 AC: 81 AN: 10628

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0186 AC: 1268 AN: 68014

Other (OTH) AF: 0.0671 AC: 142 AN: 2116

Alfa AF: 0.0357 Hom.: 248

Bravo AF: 0.0674

Asia WGS AF: 0.114 AC: 396 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	1.2
DANN	Benign	0.54
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10504435; hg19: chr8-69900903;