4-187615604-C-G

Variant names:

• chr4-187615604-C-G
• rs1876071
• ENST00000663333.1:n.267C>G

Variant summary

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

The ENST00000663333.1(ENSG00000249642):​n.267C>G 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 0.69 in 151,886 control chromosomes in the GnomAD database, including 36,412 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 0.69 (36412 hom., cov: 30)
• Consequence: ENSG00000249642 ENST00000663333.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 1 publications found

Genes affected

ENSG00000249642 (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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663333.1. 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
	LINC02492	NR_110436.1		n.157+50158G>C		intron	N/A
	LOC105377603	NR_188471.1		n.273+1605C>G		intron	N/A
	LOC105377603	NR_188472.1		n.273+1605C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249642	ENST00000663333.1		n.267C>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000249642	ENST00000505488.3	TSL:3	n.433+1605C>G		intron	N/A
	LINC02492	ENST00000507817.3	TSL:2	n.271+50158G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104782 AN: 151768 Hom.: 36388 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.690 AC: 104864 AN: 151886 Hom.: 36412 Cov.: 30 AF XY: 0.691 AC XY: 51295 AN XY: 74234

African (AFR) AF: 0.671 AC: 27786 AN: 41398

American (AMR) AF: 0.648 AC: 9880 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3468

East Asian (EAS) AF: 0.977 AC: 5035 AN: 5152

South Asian (SAS) AF: 0.789 AC: 3798 AN: 4812

European-Finnish (FIN) AF: 0.654 AC: 6886 AN: 10528

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

European-Non Finnish (NFE) AF: 0.687 AC: 46664 AN: 67958

Other (OTH) AF: 0.711 AC: 1500 AN: 2110

Alfa AF: 0.563 Hom.: 1517

Bravo AF: 0.691

Asia WGS AF: 0.865 AC: 3007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs1876071; hg19: chr4-188536758;