ENST00000567777.2:n.408-67390G>A

Variant names:

• chr16-76844965-G-A
• rs13330107
• ENST00000567777.2:n.408-67390G>A

Variant summary

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

The ENST00000567777.2(LINC02125):​n.408-67390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,982 control chromosomes in the GnomAD database, including 9,523 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 0.35 (9523 hom., cov: 32)
• Consequence: LINC02125 ENST00000567777.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 11 publications found

Genes affected

LINC02125 (HGNC:52982): (long intergenic non-protein coding RNA 2125)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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
LINC02125	ENST00000567777.2	n.408-67390G>A		intron_variant	Intron 3 of 4	3
LINC02125	ENST00000751836.1	n.502-67390G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53528 AN: 151864 Hom.: 9514 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.352 AC: 53567 AN: 151982 Hom.: 9523 Cov.: 32 AF XY: 0.345 AC XY: 25598 AN XY: 74290

African (AFR) AF: 0.376 AC: 15559 AN: 41418

American (AMR) AF: 0.279 AC: 4260 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1441 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1720 AN: 5156

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4814

European-Finnish (FIN) AF: 0.284 AC: 3007 AN: 10572

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25147 AN: 67950

Other (OTH) AF: 0.370 AC: 783 AN: 2114

Alfa AF: 0.363 Hom.: 38614

Bravo AF: 0.354

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.44
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs13330107; hg19: chr16-76878862;