rs270654

Variant names:

• chr5-159138101-T-C
• rs270654
• ENST00000826187.1:n.208-23248T>C

Variant summary

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

The ENST00000826187.1(LINC02202):​n.208-23248T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0715 in 152,292 control chromosomes in the GnomAD database, including 511 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 0.072 (511 hom., cov: 32)
• Consequence: LINC02202 ENST00000826187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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.208-23248T>C		intron_variant	Intron 1 of 2
LINC02202	ENST00000826188.1	n.162-23248T>C		intron_variant	Intron 1 of 1
LINC02202	ENST00000826189.1	n.110+1918T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10896 AN: 152174 Hom.: 511 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0715 AC: 10889 AN: 152292 Hom.: 511 Cov.: 32 AF XY: 0.0697 AC XY: 5188 AN XY: 74470

African (AFR) AF: 0.0188 AC: 781 AN: 41574

American (AMR) AF: 0.0641 AC: 981 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0763 AC: 265 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0617 AC: 298 AN: 4830

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7263 AN: 68018

Other (OTH) AF: 0.0810 AC: 171 AN: 2112

Alfa AF: 0.0941 Hom.: 1387

Bravo AF: 0.0657

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.62
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs270654; hg19: chr5-158565109; COSMIC: COSV60222470;