5-159129730-T-C

Variant names:

• chr5-159129730-T-C
• rs270664
• ENST00000826187.1:n.207+28892T>C

Variant summary

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

The ENST00000826187.1(LINC02202):​n.207+28892T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,890 control chromosomes in the GnomAD database, including 27,541 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 0.59 (27541 hom., cov: 30)
• Consequence: LINC02202 ENST00000826187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 9 publications found

Genes affected

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

ENSG00000307478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826187.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02202	ENST00000826187.1		n.207+28892T>C		intron	N/A
	LINC02202	ENST00000826188.1		n.161+28892T>C		intron	N/A
	LINC02202	ENST00000826189.1		n.58-6401T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89447 AN: 151770 Hom.: 27503 Cov.: 30

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.589 AC: 89536 AN: 151890 Hom.: 27541 Cov.: 30 AF XY: 0.590 AC XY: 43815 AN XY: 74200

African (AFR) AF: 0.763 AC: 31609 AN: 41426

American (AMR) AF: 0.621 AC: 9474 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5162

South Asian (SAS) AF: 0.541 AC: 2605 AN: 4816

European-Finnish (FIN) AF: 0.523 AC: 5488 AN: 10500

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34246 AN: 67946

Other (OTH) AF: 0.596 AC: 1253 AN: 2102

Alfa AF: 0.534 Hom.: 58574

Bravo AF: 0.602

Asia WGS AF: 0.549 AC: 1910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.52
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs270664; hg19: chr5-158556738;