rs12505439

Variant names:

• chr4-138380590-G-A
• rs12505439
• ENST00000507145.1:n.243+19188G>A

Variant summary

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

The ENST00000507145.1(LINC00499):​n.243+19188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,946 control chromosomes in the GnomAD database, including 5,929 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 0.27 (5929 hom., cov: 32)
• Consequence: LINC00499 ENST00000507145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00499	NR_051987.1	n.244+19188G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00499	ENST00000507145.1	n.243+19188G>A		intron_variant	Intron 2 of 2	4
LINC00499	ENST00000510736.1	n.485+30740G>A		intron_variant	Intron 3 of 3	5
LINC00499	ENST00000653577.1	n.485+30740G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40985 AN: 151828 Hom.: 5928 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.270 AC: 40998 AN: 151946 Hom.: 5929 Cov.: 32 AF XY: 0.272 AC XY: 20183 AN XY: 74246

African (AFR) AF: 0.200 AC: 8309 AN: 41452

American (AMR) AF: 0.191 AC: 2910 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1132 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1054 AN: 5150

South Asian (SAS) AF: 0.445 AC: 2145 AN: 4818

European-Finnish (FIN) AF: 0.325 AC: 3427 AN: 10534

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21081 AN: 67954

Other (OTH) AF: 0.293 AC: 620 AN: 2114

Alfa AF: 0.293 Hom.: 29144

Bravo AF: 0.251

Asia WGS AF: 0.319 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.84
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs12505439; hg19: chr4-139301744;