chr16-76854379-G-A

Variant names:

• chr16-76854379-G-A
• rs7196352
• ENST00000567777.2:n.408-57976G>A

Variant summary

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

The ENST00000567777.2(LINC02125):​n.408-57976G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,902 control chromosomes in the GnomAD database, including 15,646 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 0.45 (15646 hom., cov: 32)
• Consequence: LINC02125 ENST00000567777.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 1 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 = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567777.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02125	ENST00000567777.2	TSL:3	n.408-57976G>A		intron	N/A
	LINC02125	ENST00000751836.1		n.502-57976G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67574 AN: 151784 Hom.: 15622 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.445 AC: 67655 AN: 151902 Hom.: 15646 Cov.: 32 AF XY: 0.445 AC XY: 33023 AN XY: 74256

African (AFR) AF: 0.554 AC: 22948 AN: 41424

American (AMR) AF: 0.504 AC: 7695 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1520 AN: 3462

East Asian (EAS) AF: 0.174 AC: 893 AN: 5144

South Asian (SAS) AF: 0.412 AC: 1981 AN: 4814

European-Finnish (FIN) AF: 0.343 AC: 3625 AN: 10562

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.404 AC: 27474 AN: 67928

Other (OTH) AF: 0.428 AC: 904 AN: 2110

Alfa AF: 0.439 Hom.: 2386

Bravo AF: 0.460

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.28
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs7196352; hg19: chr16-76888276;