2-64980940-G-A

Position:

• chr2-64980940-G-A

Variant summary

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

The ENST00000653778.1(LINC02245):​n.513+67014C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02245	ENST00000653778.1	n.513+67014C>T		intron_variant, non_coding_transcript_variant
LINC02245	ENST00000669631.1	n.227-10155C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.512

Alfa AF: 0.437 Hom.: 6453

Bravo AF: 0.544

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10211524; hg19: chr2-65208074;