5-159133146-C-T

Variant names:

• chr5-159133146-C-T
• rs270661
• ENST00000826187.1:n.208-28203C>T

Variant summary

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

The ENST00000826187.1(LINC02202):​n.208-28203C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,190 control chromosomes in the GnomAD database, including 2,507 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 0.18 (2507 hom., cov: 32)
• Consequence: LINC02202 ENST00000826187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 9 publications found

Genes affected

LINC02202 (HGNC:53068): (long intergenic non-protein coding RNA 2202)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02202	ENST00000826187.1	n.208-28203C>T		intron_variant	Intron 1 of 2
LINC02202	ENST00000826188.1	n.162-28203C>T		intron_variant	Intron 1 of 1
LINC02202	ENST00000826189.1	n.58-2985C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27302 AN: 152072 Hom.: 2500 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.180 AC: 27327 AN: 152190 Hom.: 2507 Cov.: 32 AF XY: 0.177 AC XY: 13177 AN XY: 74408

African (AFR) AF: 0.182 AC: 7547 AN: 41512

American (AMR) AF: 0.130 AC: 1990 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.135 AC: 697 AN: 5172

South Asian (SAS) AF: 0.240 AC: 1158 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10596

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13210 AN: 68006

Other (OTH) AF: 0.180 AC: 380 AN: 2116

Alfa AF: 0.181 Hom.: 4408

Bravo AF: 0.174

Asia WGS AF: 0.166 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.75
DANN	Benign	0.95
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs270661; hg19: chr5-158560154; COSMIC: COSV60222392;