rs426029

Variant names:

• chr4-138364610-G-A
• rs426029
• ENST00000507145.1:n.243+3208G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-138364610-G-A
• chr4-138364610-G-T

Variant summary

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

The ENST00000507145.1(LINC00499):​n.243+3208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,820 control chromosomes in the GnomAD database, including 9,782 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 0.34 (9782 hom., cov: 32)
• Consequence: LINC00499 ENST00000507145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507145.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00499	NR_051987.1		n.244+3208G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00499	ENST00000507145.1	TSL:4	n.243+3208G>A		intron	N/A
	LINC00499	ENST00000510736.1	TSL:5	n.485+14760G>A		intron	N/A
	LINC00499	ENST00000653577.1		n.485+14760G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52245 AN: 151702 Hom.: 9776 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.344 AC: 52280 AN: 151820 Hom.: 9782 Cov.: 32 AF XY: 0.347 AC XY: 25729 AN XY: 74170

African (AFR) AF: 0.222 AC: 9180 AN: 41438

American (AMR) AF: 0.284 AC: 4331 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1357 AN: 3466

East Asian (EAS) AF: 0.193 AC: 995 AN: 5162

South Asian (SAS) AF: 0.539 AC: 2599 AN: 4818

European-Finnish (FIN) AF: 0.427 AC: 4504 AN: 10544

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28036 AN: 67846

Other (OTH) AF: 0.361 AC: 762 AN: 2112

Alfa AF: 0.378 Hom.: 31062

Bravo AF: 0.321

Asia WGS AF: 0.359 AC: 1247 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.60
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs426029; hg19: chr4-139285764;