rs890447

chr4-138339831-G-A

Variant summary

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

The NR_051987.1(LINC00499):n.138-21465G>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 0.0669 in 152,128 control chromosomes in the GnomAD database, including 860 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 0.067 (860 hom., cov: 32)
• Consequence: LINC00499 NR_051987.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

LINC00499 (HGNC:43436): (long intergenic non-protein coding RNA 499)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00499	NR_051987.1	n.138-21465G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00499	ENST00000663528.1	n.319+574G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10181 AN: 152010 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.0765

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0748

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

GnomAD4 genome AF: 0.0669 AC: 10184 AN: 152128 Hom.: 860 Cov.: 32 AF XY: 0.0738 AC XY: 5490 AN XY: 74358

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.0765

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0769

Alfa AF: 0.0570 Hom.: 266

Bravo AF: 0.0794

Asia WGS AF: 0.181 AC: 626 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs890447; hg19: chr4-139260985;