16-76856229-T-C

Variant names:

• chr16-76856229-T-C
• rs17679567
• ENST00000567777.2:n.408-56126T>C

Variant summary

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

The ENST00000567777.2(LINC02125):​n.408-56126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,076 control chromosomes in the GnomAD database, including 3,020 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 0.19 (3020 hom., cov: 33)
• Consequence: LINC02125 ENST00000567777.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02125	ENST00000567777.2	TSL:3	n.408-56126T>C		intron	N/A
	LINC02125	ENST00000751836.1		n.502-56126T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29481 AN: 151958 Hom.: 3013 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.194 AC: 29513 AN: 152076 Hom.: 3020 Cov.: 33 AF XY: 0.192 AC XY: 14254 AN XY: 74352

African (AFR) AF: 0.160 AC: 6644 AN: 41512

American (AMR) AF: 0.176 AC: 2685 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3470

East Asian (EAS) AF: 0.0301 AC: 155 AN: 5158

South Asian (SAS) AF: 0.127 AC: 611 AN: 4816

European-Finnish (FIN) AF: 0.227 AC: 2397 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15447 AN: 67950

Other (OTH) AF: 0.197 AC: 415 AN: 2106

Alfa AF: 0.214 Hom.: 10959

Bravo AF: 0.188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.89
DANN	Benign	0.40
PhyloP100		0.081

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17679567;

hg19: chr16-76890126;