rs10520462

Variant names:

• chr4-181103950-C-T
• rs10520462
• ENST00000512487.2:n.526-39470G>A

Variant summary

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

The ENST00000512487.2(LINC00290):​n.526-39470G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,606 control chromosomes in the GnomAD database, including 2,633 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 0.18 (2633 hom., cov: 31)
• Consequence: LINC00290 ENST00000512487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 4 publications found

Genes affected

LINC00290 (HGNC:38515): (long intergenic non-protein coding RNA 290)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00290	NR_033918.1	n.202-39470G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00290	ENST00000512487.2	n.526-39470G>A		intron_variant	Intron 2 of 2	1
LINC00290	ENST00000778348.1	n.288-39470G>A		intron_variant	Intron 2 of 3
LINC00290	ENST00000778349.1	n.236-39470G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27311 AN: 151490 Hom.: 2626 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.180 AC: 27344 AN: 151606 Hom.: 2633 Cov.: 31 AF XY: 0.179 AC XY: 13263 AN XY: 74048

African (AFR) AF: 0.177 AC: 7312 AN: 41352

American (AMR) AF: 0.120 AC: 1827 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 591 AN: 3466

East Asian (EAS) AF: 0.179 AC: 920 AN: 5142

South Asian (SAS) AF: 0.240 AC: 1153 AN: 4812

European-Finnish (FIN) AF: 0.161 AC: 1691 AN: 10476

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13274 AN: 67850

Other (OTH) AF: 0.173 AC: 365 AN: 2108

Alfa AF: 0.192 Hom.: 1638

Bravo AF: 0.173

Asia WGS AF: 0.183 AC: 634 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.47
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs10520462; hg19: chr4-182025103;