16-9287105-A-G

Variant names:

• chr16-9287105-A-G
• rs1213205
• ENST00000784364.1:n.-58A>G

Variant summary

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

The ENST00000784364.1(LINC02177):​n.-58A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,910 control chromosomes in the GnomAD database, including 30,456 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 0.62 (30456 hom., cov: 31)
• Consequence: LINC02177 ENST00000784364.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 7 publications found

Genes affected

LINC02177 (HGNC:53039): (long intergenic non-protein coding RNA 2177)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784364.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02177	ENST00000784364.1		n.-58A>G		upstream_gene	N/A
	LINC02177	ENST00000784365.1		n.-63A>G		upstream_gene	N/A
	LINC02177	ENST00000784366.1		n.-79A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94705 AN: 151792 Hom.: 30442 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.624 AC: 94749 AN: 151910 Hom.: 30456 Cov.: 31 AF XY: 0.625 AC XY: 46379 AN XY: 74230

African (AFR) AF: 0.447 AC: 18518 AN: 41416

American (AMR) AF: 0.732 AC: 11161 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2337 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3806 AN: 5152

South Asian (SAS) AF: 0.658 AC: 3165 AN: 4808

European-Finnish (FIN) AF: 0.669 AC: 7052 AN: 10548

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46530 AN: 67946

Other (OTH) AF: 0.674 AC: 1423 AN: 2112

Alfa AF: 0.656 Hom.: 18097

Bravo AF: 0.623

Asia WGS AF: 0.679 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.67
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1213205; hg19: chr16-9380962;