rs10520464

chr4-181065282-G-C

Variant summary

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

The NR_033918.1(LINC00290):n.202-802C>G variant causes a intron, non coding transcript 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 NR_033918.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00290	NR_033918.1	n.202-802C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00290	ENST00000512487.1	n.202-802C>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.424

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520464; hg19: chr4-181986435;