ENST00000499583.2:n.211-1748A>G

Variant names:

• chr5-159110111-A-G
• rs2161357
• ENST00000499583.2:n.211-1748A>G

Variant summary

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

The ENST00000499583.2(LINC02202):​n.211-1748A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,194 control chromosomes in the GnomAD database, including 2,247 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 0.16 (2247 hom., cov: 32)
• Consequence: LINC02202 ENST00000499583.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02202	NR_109890.1	n.357-1748A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02202	ENST00000499583.2	n.211-1748A>G		intron_variant	Intron 1 of 2	2
LINC02202	ENST00000517335.3	n.357-1765A>G		intron_variant	Intron 1 of 2	4
LINC02202	ENST00000826187.1	n.207+9273A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24549 AN: 152076 Hom.: 2244 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.161 AC: 24572 AN: 152194 Hom.: 2247 Cov.: 32 AF XY: 0.161 AC XY: 11968 AN XY: 74384

African (AFR) AF: 0.102 AC: 4226 AN: 41536

American (AMR) AF: 0.168 AC: 2578 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3470

East Asian (EAS) AF: 0.0279 AC: 145 AN: 5190

South Asian (SAS) AF: 0.0736 AC: 355 AN: 4822

European-Finnish (FIN) AF: 0.255 AC: 2695 AN: 10572

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13534 AN: 67990

Other (OTH) AF: 0.157 AC: 332 AN: 2110

Alfa AF: 0.181 Hom.: 4534

Bravo AF: 0.152

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2161357; hg19: chr5-158537119;