chr16-76716223-T-C

Variant names:

• chr16-76716223-T-C
• rs8057477
• ENST00000563764.2:n.*122+80600T>C

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*122+80600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,906 control chromosomes in the GnomAD database, including 10,467 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 0.37 (10467 hom., cov: 31)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 3 publications found

Genes affected

ENSG00000287694 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563764.2. 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
	ENSG00000287694	ENST00000563764.2	TSL:3	n.*122+80600T>C		intron	N/A	ENSP00000455258.1
	LINC02125	ENST00000567777.2	TSL:3	n.245-20094T>C		intron	N/A
	LINC02125	ENST00000751836.1		n.339-20094T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55506 AN: 151788 Hom.: 10454 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.366 AC: 55548 AN: 151906 Hom.: 10467 Cov.: 31 AF XY: 0.365 AC XY: 27118 AN XY: 74226

African (AFR) AF: 0.425 AC: 17606 AN: 41424

American (AMR) AF: 0.410 AC: 6259 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1956 AN: 5118

South Asian (SAS) AF: 0.364 AC: 1755 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2970 AN: 10562

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22666 AN: 67944

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.344 Hom.: 1504

Bravo AF: 0.376

Asia WGS AF: 0.383 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8057477; hg19: chr16-76750120;