rs2302270

Variant names:

• chr12-126427497-G-A
• rs2302270
• ENST00000544419.1:n.346+230G>A

Variant summary

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

The ENST00000544419.1(LINC02350):​n.346+230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,116 control chromosomes in the GnomAD database, including 2,145 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 (2145 hom., cov: 32)
• Consequence: LINC02350 ENST00000544419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 3 publications found

Genes affected

LINC02350 (HGNC:53272): (long intergenic non-protein coding RNA 2350)

LINC02825 (HGNC:27477): (long intergenic non-protein coding RNA 2825)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02350	NR_146291.1	n.125+230G>A		intron_variant	Intron 2 of 2
LINC02825	NR_147498.1	n.259+17923C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02350	ENST00000544419.1	n.346+230G>A		intron_variant	Intron 2 of 2	3
LINC02350	ENST00000642569.1	n.1449-6378G>A		intron_variant	Intron 9 of 9
LINC02350	ENST00000718399.1	n.44-11458G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25169 AN: 151998 Hom.: 2139 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.166 AC: 25196 AN: 152116 Hom.: 2145 Cov.: 32 AF XY: 0.166 AC XY: 12334 AN XY: 74356

African (AFR) AF: 0.189 AC: 7853 AN: 41502

American (AMR) AF: 0.123 AC: 1888 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3468

East Asian (EAS) AF: 0.127 AC: 657 AN: 5166

South Asian (SAS) AF: 0.162 AC: 780 AN: 4816

European-Finnish (FIN) AF: 0.204 AC: 2157 AN: 10564

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10961 AN: 67994

Other (OTH) AF: 0.155 AC: 327 AN: 2110

Alfa AF: 0.160 Hom.: 3960

Bravo AF: 0.163

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2302270; hg19: chr12-126912043;