2-65055574-G-C

Variant names:

• chr2-65055574-G-C
• rs6728523
• ENST00000653778.1:n.254+341C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653778.1(LINC02245):​n.254+341C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,052 control chromosomes in the GnomAD database, including 6,492 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 (6492 hom., cov: 33)
• Consequence: LINC02245 ENST00000653778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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.254+341C>G		intron_variant	Intron 1 of 3
LINC02245	ENST00000666526.2	n.312+341C>G		intron_variant	Intron 1 of 1
LINC02245	ENST00000685506.2	n.291+341C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43457 AN: 151934 Hom.: 6470 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.286 AC: 43524 AN: 152052 Hom.: 6492 Cov.: 33 AF XY: 0.284 AC XY: 21083 AN XY: 74322

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.310

Alfa AF: 0.281 Hom.: 775

Bravo AF: 0.293

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	-0.89
CADD	Benign	9.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6728523; hg19: chr2-65282708;