rs2540969

Variant names:

• chr2-65028006-A-G
• rs2540969
• ENST00000653778.1:n.513+19948T>C

Variant summary

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

The ENST00000653778.1(LINC02245):​n.513+19948T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.291 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+19948T>C		intron_variant	Intron 2 of 3
LINC02245	ENST00000669631.1	n.226+19948T>C		intron_variant	Intron 1 of 4
LINC02245	ENST00000771808.1	n.573+19948T>C		intron_variant	Intron 2 of 6

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

African (AFR) AF: 0.295 AC: 12230 AN: 41442

American (AMR) AF: 0.124 AC: 1892 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3472

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5188

South Asian (SAS) AF: 0.120 AC: 577 AN: 4816

European-Finnish (FIN) AF: 0.118 AC: 1252 AN: 10566

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9133 AN: 67984

Other (OTH) AF: 0.163 AC: 344 AN: 2110

Alfa AF: 0.162 Hom.: 291

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2540969; hg19: chr2-65255140;