12-127330541-C-T

Variant names:

• chr12-127330541-C-T
• rs2656824
• ENST00000545739.2:n.227+3519G>A

Variant summary

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

The ENST00000545739.2(LINC02375):​n.227+3519G>A variant causes a intron 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 ENST00000545739.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 5 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 = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02375	NR_110057.1	n.201+3519G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02375	ENST00000545739.2	n.227+3519G>A		intron_variant	Intron 2 of 2	1
LINC02375	ENST00000657634.2	n.293+3519G>A		intron_variant	Intron 2 of 2
LINC02375	ENST00000670647.2	n.281+3519G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.276 AC: 11445 AN: 41434

American (AMR) AF: 0.260 AC: 3971 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3470

East Asian (EAS) AF: 0.0337 AC: 174 AN: 5170

South Asian (SAS) AF: 0.183 AC: 883 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2686 AN: 10588

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17829 AN: 67962

Other (OTH) AF: 0.237 AC: 502 AN: 2114

Alfa AF: 0.257 Hom.: 16116

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
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs2656824; hg19: chr12-127815086;