4-145341595-C-T

Variant names:

• chr4-145341595-C-T
• rs568752
• ENST00000654926.1:n.110+1855G>A

Variant summary

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

The ENST00000654926.1(LINC02266):​n.110+1855G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,036 control chromosomes in the GnomAD database, including 29,177 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 0.61 (29177 hom., cov: 31)
• Consequence: LINC02266 ENST00000654926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 7 publications found

Genes affected

LINC02266 (HGNC:53180): (long intergenic non-protein coding RNA 2266)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654926.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02266	ENST00000654926.1		n.110+1855G>A		intron	N/A
	LINC02266	ENST00000659559.1		n.125+1840G>A		intron	N/A
	LINC02266	ENST00000768763.1		n.111-2511G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93017 AN: 151918 Hom.: 29147 Cov.: 31

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.612 AC: 93101 AN: 152036 Hom.: 29177 Cov.: 31 AF XY: 0.617 AC XY: 45880 AN XY: 74304

African (AFR) AF: 0.724 AC: 30041 AN: 41472

American (AMR) AF: 0.551 AC: 8412 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3472

East Asian (EAS) AF: 0.800 AC: 4147 AN: 5186

South Asian (SAS) AF: 0.617 AC: 2967 AN: 4812

European-Finnish (FIN) AF: 0.647 AC: 6829 AN: 10556

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36940 AN: 67956

Other (OTH) AF: 0.597 AC: 1257 AN: 2106

Alfa AF: 0.573 Hom.: 48207

Bravo AF: 0.610

Asia WGS AF: 0.683 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.38
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs568752; hg19: chr4-146262747;