rs4765531

chr12-127331658-C-Achr12-127331658-C-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+2402G>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 0.295 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 NR_110057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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=-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/exons	MANE	UniProt
LINC02375	NR_110057.1	n.201+2402G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02375	ENST00000545739.2	n.227+2402G>T		intron_variant, non_coding_transcript_variant		1
LINC02375	ENST00000657634.1	n.293+2402G>T		intron_variant, non_coding_transcript_variant
LINC02375	ENST00000670647.1	n.269+2402G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.272

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4765531; hg19: chr12-127816203;