ENST00000653778.1:n.513+67014C>T

Variant names:

• chr2-64980940-G-A
• rs10211524
• ENST00000653778.1:n.513+67014C>T

Variant summary

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

The ENST00000653778.1(LINC02245):​n.513+67014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,086 control chromosomes in the GnomAD database, including 21,343 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 0.51 (21343 hom., cov: 33)
• Consequence: LINC02245 ENST00000653778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 30 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653778.1. 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
	LINC02245	ENST00000653778.1		n.513+67014C>T		intron	N/A
	LINC02245	ENST00000669631.1		n.227-10155C>T		intron	N/A
	LINC02245	ENST00000771808.1		n.574-24956C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78217 AN: 151966 Hom.: 21318 Cov.: 33

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.515 AC: 78288 AN: 152086 Hom.: 21343 Cov.: 33 AF XY: 0.515 AC XY: 38310 AN XY: 74356

African (AFR) AF: 0.653 AC: 27101 AN: 41480

American (AMR) AF: 0.599 AC: 9167 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4193 AN: 5184

South Asian (SAS) AF: 0.355 AC: 1713 AN: 4826

European-Finnish (FIN) AF: 0.410 AC: 4336 AN: 10566

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28745 AN: 67958

Other (OTH) AF: 0.512 AC: 1076 AN: 2102

Alfa AF: 0.438 Hom.: 7204

Bravo AF: 0.544

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.72
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10211524; hg19: chr2-65208074;