rs2540969

chr2-65028006-A-G

Variant summary

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

The ENST00000653778.1(LINC02245):n.513+19948T>C 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 0.172 in 152,070 control chromosomes in the GnomAD database, including 2,730 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 0.17 (2730 hom., cov: 32)
• Consequence: LINC02245 ENST00000653778.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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 (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02245	ENST00000653778.1	n.513+19948T>C		intron_variant, non_coding_transcript_variant
LINC02245	ENST00000669631.1	n.226+19948T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26107 AN: 151952 Hom.: 2730 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.172 AC: 26121 AN: 152070 Hom.: 2730 Cov.: 32 AF XY: 0.167 AC XY: 12440 AN XY: 74330

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.163

Alfa AF: 0.156 Hom.: 260

Bravo AF: 0.176

Asia WGS AF: 0.0770 AC: 270 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	0.20
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2540969; hg19: chr2-65255140;