rs2302647

Variant names:

• chr2-65056040-G-A
• rs2302647
• ENST00000653778.1:n.129C>T

Variant summary

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

The ENST00000653778.1(LINC02245):​n.129C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,236 control chromosomes in the GnomAD database, including 6,449 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 0.29 (6449 hom., cov: 33)
• Consequence: LINC02245 ENST00000653778.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817
• Publications: 10 publications found

Genes affected

LINC02245 (HGNC:53134): (long intergenic non-protein coding RNA 2245)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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
LINC02245	ENST00000653778.1	n.129C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LINC02245	ENST00000666526.3	n.188C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LINC02245	ENST00000685506.3	n.168C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43359 AN: 152118 Hom.: 6427 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.285 AC: 43426 AN: 152236 Hom.: 6449 Cov.: 33 AF XY: 0.283 AC XY: 21056 AN XY: 74426

African (AFR) AF: 0.345 AC: 14339 AN: 41538

American (AMR) AF: 0.273 AC: 4175 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1676 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4822

European-Finnish (FIN) AF: 0.212 AC: 2247 AN: 10602

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17194 AN: 68008

Other (OTH) AF: 0.309 AC: 653 AN: 2116

Alfa AF: 0.272 Hom.: 24118

Bravo AF: 0.292

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.1
DANN	Benign	0.85
PhyloP100		0.82
PromoterAI		0.0041	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2302647; hg19: chr2-65283174;