ENST00000748298.1:n.535+2694T>C

Variant names:

• chr12-127341563-A-G
• rs11835432
• ENST00000748298.1:n.535+2694T>C

Variant summary

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

The ENST00000748298.1(LINC02375):​n.535+2694T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,168 control chromosomes in the GnomAD database, including 2,641 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 0.18 (2641 hom., cov: 32)
• Consequence: LINC02375 ENST00000748298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02375	ENST00000748298.1	n.535+2694T>C		intron_variant	Intron 2 of 3
LINC02375	ENST00000748299.1	n.535+2694T>C		intron_variant	Intron 2 of 3
LINC02375	ENST00000748300.1	n.99+1330T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27788 AN: 152050 Hom.: 2643 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.183 AC: 27806 AN: 152168 Hom.: 2641 Cov.: 32 AF XY: 0.180 AC XY: 13377 AN XY: 74394

African (AFR) AF: 0.166 AC: 6882 AN: 41530

American (AMR) AF: 0.215 AC: 3290 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3466

East Asian (EAS) AF: 0.00366 AC: 19 AN: 5190

South Asian (SAS) AF: 0.129 AC: 621 AN: 4822

European-Finnish (FIN) AF: 0.189 AC: 2001 AN: 10590

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13801 AN: 67976

Other (OTH) AF: 0.180 AC: 381 AN: 2114

Alfa AF: 0.195 Hom.: 9633

Bravo AF: 0.185

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.49
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11835432; hg19: chr12-127826108;