chr16-86715176-C-G

Variant names:

• chr16-86715176-C-G
• rs177267
• ENST00000647615.1:n.87-69C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647615.1(LINC02188):​n.87-69C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,876 control chromosomes in the GnomAD database, including 6,734 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 0.29 (6734 hom., cov: 31)
• Consequence: LINC02188 ENST00000647615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

Genes affected

LINC02188 (HGNC:53050): (long intergenic non-protein coding RNA 2188)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 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
LINC02188	ENST00000647615.1	n.87-69C>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44208 AN: 151758 Hom.: 6732 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.291 AC: 44232 AN: 151876 Hom.: 6734 Cov.: 31 AF XY: 0.293 AC XY: 21776 AN XY: 74206

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.284

Alfa AF: 0.311 Hom.: 927

Bravo AF: 0.285

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs177267; hg19: chr16-86748782;