rs2593270

Positions:

• chr12-127330633-G-A
• chr12-127330633-G-T

Variant summary

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

The NR_110057.1(LINC02375):​n.201+3427C>T 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 0.338 in 152,096 control chromosomes in the GnomAD database, including 10,385 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 0.34 (10385 hom., cov: 32)
• Consequence: LINC02375 NR_110057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02375	NR_110057.1	n.201+3427C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02375	ENST00000545739.2	n.227+3427C>T		intron_variant, non_coding_transcript_variant		1
LINC02375	ENST00000657634.1	n.293+3427C>T		intron_variant, non_coding_transcript_variant
LINC02375	ENST00000670647.1	n.269+3427C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51361 AN: 151976 Hom.: 10365 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0335

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.338 AC: 51422 AN: 152096 Hom.: 10385 Cov.: 32 AF XY: 0.332 AC XY: 24720 AN XY: 74360

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0332

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.302

Alfa AF: 0.258 Hom.: 3715

Bravo AF: 0.353

Asia WGS AF: 0.142 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2593270; hg19: chr12-127815178;