rs10520464

Variant names:

• chr4-181065282-G-C
• rs10520464
• ENST00000512487.2:n.526-802C>G

Variant summary

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

The ENST00000512487.2(LINC00290):​n.526-802C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,864 control chromosomes in the GnomAD database, including 10,295 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 0.36 (10295 hom., cov: 32)
• Consequence: LINC00290 ENST00000512487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00290	NR_033918.1	n.202-802C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00290	ENST00000512487.2	n.526-802C>G		intron_variant	Intron 2 of 2	1
LINC00290	ENST00000778348.1	n.288-802C>G		intron_variant	Intron 2 of 3
LINC00290	ENST00000778349.1	n.236-802C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53945 AN: 151746 Hom.: 10306 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.355 AC: 53944 AN: 151864 Hom.: 10295 Cov.: 32 AF XY: 0.354 AC XY: 26287 AN XY: 74200

African (AFR) AF: 0.221 AC: 9170 AN: 41410

American (AMR) AF: 0.470 AC: 7171 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1630 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2337 AN: 5138

South Asian (SAS) AF: 0.377 AC: 1819 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3450 AN: 10536

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.397 AC: 26991 AN: 67926

Other (OTH) AF: 0.424 AC: 892 AN: 2106

Alfa AF: 0.362 Hom.: 1298

Bravo AF: 0.364

Asia WGS AF: 0.394 AC: 1367 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.2
DANN	Benign	0.69
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs10520464; hg19: chr4-181986435;