ENST00000664556.1:n.988G>A

Variant names:

• chr4-138339831-G-A
• rs890447
• ENST00000664556.1:n.988G>A

Variant summary

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

The ENST00000664556.1(LINC00499):​n.988G>A variant causes a non coding transcript exon 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 ENST00000664556.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664556.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00499	NR_051987.1		n.138-21465G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00499	ENST00000664556.1		n.988G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00499	ENST00000507145.1	TSL:4	n.137-21465G>A		intron	N/A
	LINC00499	ENST00000510736.1	TSL:5	n.352+574G>A		intron	N/A

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

African (AFR) AF: 0.0137 AC: 567 AN: 41514

American (AMR) AF: 0.216 AC: 3303 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1830 AN: 5162

South Asian (SAS) AF: 0.0766 AC: 369 AN: 4820

European-Finnish (FIN) AF: 0.0765 AC: 809 AN: 10572

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2994 AN: 68004

Other (OTH) AF: 0.0769 AC: 162 AN: 2108

Alfa AF: 0.0560 Hom.: 278

Bravo AF: 0.0794

Asia WGS AF: 0.181 AC: 626 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs890447; hg19: chr4-139260985;