chr4-187615308-A-G

Position:

• chr4-187615308-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900879	XR_007058510.1	n.415T>C		non_coding_transcript_exon_variant	1/2
LINC02492	NR_110436.1	n.157+50454T>C		intron_variant, non_coding_transcript_variant
LOC105377603	XR_001741957.2	n.304+1309A>G		intron_variant, non_coding_transcript_variant
LOC105377604	XR_939614.3	n.156-22381T>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+50454T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000661504.1	n.270+1309A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.688

Alfa AF: 0.685 Hom.: 58810

Bravo AF: 0.650

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876072; hg19: chr4-188536462;