4-187615308-A-G

Variant names:

• chr4-187615308-A-G
• rs1876072
• XR_007058510.1:n.415T>C

Variant summary

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

The XR_007058510.1(LOC124900879):​n.415T>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 0.653 in 151,886 control chromosomes in the GnomAD database, including 32,627 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 0.65 (32627 hom., cov: 31)
• Consequence: LOC124900879 XR_007058510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 3 publications found

Genes affected

LOC124900879 (HGNC:):

LINC02492 (HGNC:53476): (long intergenic non-protein coding RNA 2492)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505488.3. 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
	LINC02492	NR_110436.1		n.157+50454T>C		intron	N/A
	LOC105377603	NR_188471.1		n.273+1309A>G		intron	N/A
	LOC105377603	NR_188472.1		n.273+1309A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249642	ENST00000505488.3	TSL:3	n.433+1309A>G		intron	N/A
	LINC02492	ENST00000507817.3	TSL:2	n.271+50454T>C		intron	N/A
	LINC02492	ENST00000514767.2	TSL:3	n.161+30902T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99082 AN: 151768 Hom.: 32620 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.653 AC: 99134 AN: 151886 Hom.: 32627 Cov.: 31 AF XY: 0.652 AC XY: 48380 AN XY: 74232

African (AFR) AF: 0.570 AC: 23600 AN: 41380

American (AMR) AF: 0.623 AC: 9519 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2439 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4520 AN: 5140

South Asian (SAS) AF: 0.723 AC: 3481 AN: 4816

European-Finnish (FIN) AF: 0.639 AC: 6726 AN: 10532

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46539 AN: 67966

Other (OTH) AF: 0.688 AC: 1445 AN: 2100

Alfa AF: 0.681 Hom.: 141382

Bravo AF: 0.650

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.45
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1876072; hg19: chr4-188536462;