2-65027965-T-C

Variant names:

• chr2-65027965-T-C
• rs2540970
• ENST00000653778.1:n.513+19989A>G

Variant summary

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

The ENST00000653778.1(LINC02245):​n.513+19989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,074 control chromosomes in the GnomAD database, including 13,601 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 0.40 (13601 hom., cov: 32)
• Consequence: LINC02245 ENST00000653778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 11 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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.513+19989A>G		intron_variant	Intron 2 of 3
LINC02245	ENST00000669631.1	n.226+19989A>G		intron_variant	Intron 1 of 4
LINC02245	ENST00000771808.1	n.573+19989A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61529 AN: 151956 Hom.: 13585 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.405 AC: 61586 AN: 152074 Hom.: 13601 Cov.: 32 AF XY: 0.399 AC XY: 29694 AN XY: 74346

African (AFR) AF: 0.590 AC: 24447 AN: 41462

American (AMR) AF: 0.295 AC: 4500 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1863 AN: 5176

South Asian (SAS) AF: 0.364 AC: 1751 AN: 4814

European-Finnish (FIN) AF: 0.309 AC: 3271 AN: 10580

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23033 AN: 67972

Other (OTH) AF: 0.408 AC: 863 AN: 2116

Alfa AF: 0.369 Hom.: 10326

Bravo AF: 0.409

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.19
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2540970; hg19: chr2-65255099;