4-187615604-C-G

Position:

• chr4-187615604-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058510.1(LOC124900879):​n.119G>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 0.69 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: LOC124900879 XR_007058510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

LOC124900879 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900879	XR_007058510.1	n.119G>C		non_coding_transcript_exon_variant	1/2
LINC02492	NR_110436.1	n.157+50158G>C		intron_variant, non_coding_transcript_variant
LOC105377603	XR_001741957.2	n.304+1605C>G		intron_variant, non_coding_transcript_variant
LOC105377604	XR_939614.3	n.156-22677G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02492	ENST00000507817.2	n.271+50158G>C		intron_variant, non_coding_transcript_variant		2
	ENST00000661504.1	n.270+1605C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.711

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876071; hg19: chr4-188536758;