chr4-36611742-C-G

Variant names:

• chr4-36611742-C-G
• rs2375990
• ENST00000505298.5:n.160+3676G>C

Variant summary

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

The ENST00000505298.5(LINC02505):​n.160+3676G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 151,978 control chromosomes in the GnomAD database, including 54,570 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 0.85 (54570 hom., cov: 30)
• Consequence: LINC02505 ENST00000505298.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 3 publications found

Genes affected

LINC02505 (HGNC:53494): (long intergenic non-protein coding RNA 2505)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505298.5. 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
	LINC02505	NR_149124.1		n.124+3712G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02505	ENST00000505298.5	TSL:5	n.160+3676G>C		intron	N/A
	LINC02505	ENST00000510597.7	TSL:3	n.143+3712G>C		intron	N/A
	LINC02505	ENST00000515128.3	TSL:5	n.163+3712G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128405 AN: 151860 Hom.: 54530 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.846 AC: 128502 AN: 151978 Hom.: 54570 Cov.: 30 AF XY: 0.846 AC XY: 62797 AN XY: 74270

African (AFR) AF: 0.769 AC: 31836 AN: 41408

American (AMR) AF: 0.828 AC: 12617 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3057 AN: 3468

East Asian (EAS) AF: 0.945 AC: 4878 AN: 5160

South Asian (SAS) AF: 0.845 AC: 4071 AN: 4820

European-Finnish (FIN) AF: 0.856 AC: 9062 AN: 10592

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60121 AN: 67966

Other (OTH) AF: 0.863 AC: 1824 AN: 2114

Alfa AF: 0.854 Hom.: 6508

Bravo AF: 0.840

Asia WGS AF: 0.864 AC: 3005 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	1.9
DANN	Benign	0.51
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2375990; hg19: chr4-36613364;