12-127330541-C-T

Position:

• chr12-127330541-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+3519G>A 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 0.254 in 152,020 control chromosomes in the GnomAD database, including 5,146 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 0.25 (5146 hom., cov: 32)
• Consequence: LINC02375 NR_110057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

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 = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02375	NR_110057.1	n.201+3519G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02375	ENST00000545739.2	n.227+3519G>A		intron_variant, non_coding_transcript_variant		1
LINC02375	ENST00000657634.1	n.293+3519G>A		intron_variant, non_coding_transcript_variant
LINC02375	ENST00000670647.1	n.269+3519G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38557 AN: 151902 Hom.: 5143 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.254 AC: 38580 AN: 152020 Hom.: 5146 Cov.: 32 AF XY: 0.251 AC XY: 18680 AN XY: 74336

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0337

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.237

Alfa AF: 0.255 Hom.: 10286

Bravo AF: 0.257

Asia WGS AF: 0.124 AC: 430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2656824; hg19: chr12-127815086;