ENST00000504731.1:n.499G>C

Variant names:

• chr4-188738871-G-C
• rs6553229
• ENST00000504731.1:n.499G>C

Variant summary

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

The ENST00000504731.1(ENSG00000180015):​n.499G>C 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 0.106 in 1,612,462 control chromosomes in the GnomAD database, including 9,924 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 0.13 (1375 hom., cov: 32)
  • Exomes 𝑓: 0.10 (8549 hom.)
• Consequence: ENSG00000180015 ENST00000504731.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• Publications: 4 publications found

Genes affected

ENSG00000180015 (HGNC:):

LINC02508 (HGNC:53497): (long intergenic non-protein coding RNA 2508)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504731.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000180015	ENST00000504731.1	TSL:6	n.499G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000297134	ENST00000745747.1		n.354G>C		non_coding_transcript_exon	Exon 1 of 2
	LINC02508	ENST00000745304.1		n.191+17519G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19260 AN: 152058 Hom.: 1376 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00830

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.104 AC: 151994 AN: 1460284 Hom.: 8549 Cov.: 53 AF XY: 0.104 AC XY: 75346 AN XY: 726478

African (AFR) AF: 0.203 AC: 6801 AN: 33432

American (AMR) AF: 0.110 AC: 4937 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 3342 AN: 26136

East Asian (EAS) AF: 0.00851 AC: 338 AN: 39700

South Asian (SAS) AF: 0.0995 AC: 8576 AN: 86192

European-Finnish (FIN) AF: 0.0800 AC: 4272 AN: 53420

Middle Eastern (MID) AF: 0.161 AC: 740 AN: 4602

European-Non Finnish (NFE) AF: 0.105 AC: 116315 AN: 1111824

Other (OTH) AF: 0.111 AC: 6673 AN: 60260

GnomAD4 genome AF: 0.127 AC: 19270 AN: 152178 Hom.: 1375 Cov.: 32 AF XY: 0.122 AC XY: 9110 AN XY: 74408

African (AFR) AF: 0.203 AC: 8443 AN: 41510

American (AMR) AF: 0.104 AC: 1588 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.00851 AC: 44 AN: 5168

South Asian (SAS) AF: 0.0973 AC: 469 AN: 4818

European-Finnish (FIN) AF: 0.0714 AC: 757 AN: 10606

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7198 AN: 68000

Other (OTH) AF: 0.127 AC: 268 AN: 2112

Alfa AF: 0.116 Hom.: 156

Bravo AF: 0.134

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.8
DANN	Benign	0.58
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs6553229; hg19: chr4-189660025; COSMIC: COSV71619942;