rs10520462

Positions:

• chr4-181103950-C-T

Variant summary

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

The NR_033918.1(LINC00290):​n.202-39470G>A 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 0.18 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 NR_033918.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

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=-0.83).
• 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/exons	MANE	Protein	UniProt
LINC00290	NR_033918.1	n.202-39470G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00290	ENST00000512487.1	n.202-39470G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.173

Alfa AF: 0.192 Hom.: 1486

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520462; hg19: chr4-182025103;