ENST00000545739.2:n.227+2402G>T

Variant names:

• chr12-127331658-C-A
• rs4765531
• ENST00000545739.2:n.227+2402G>T

Variant summary

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

The ENST00000545739.2(LINC02375):​n.227+2402G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,886 control chromosomes in the GnomAD database, including 7,187 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 0.30 (7187 hom., cov: 31)
• Consequence: LINC02375 ENST00000545739.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 1 publications found

Genes affected

LINC02375 (HGNC:53297): (long intergenic non-protein coding RNA 2375)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02375	NR_110057.1	n.201+2402G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02375	ENST00000545739.2	n.227+2402G>T		intron_variant	Intron 2 of 2	1
LINC02375	ENST00000657634.2	n.293+2402G>T		intron_variant	Intron 2 of 2
LINC02375	ENST00000670647.2	n.281+2402G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44789 AN: 151768 Hom.: 7179 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.295 AC: 44830 AN: 151886 Hom.: 7187 Cov.: 31 AF XY: 0.290 AC XY: 21533 AN XY: 74224

African (AFR) AF: 0.415 AC: 17171 AN: 41390

American (AMR) AF: 0.281 AC: 4286 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3470

East Asian (EAS) AF: 0.0336 AC: 173 AN: 5156

South Asian (SAS) AF: 0.187 AC: 898 AN: 4804

European-Finnish (FIN) AF: 0.252 AC: 2659 AN: 10540

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.264 AC: 17952 AN: 67956

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.148 Hom.: 265

Bravo AF: 0.305

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4765531; hg19: chr12-127816203;