16-9288472-A-G

Variant names:

• chr16-9288472-A-G
• rs8061903
• ENST00000784364.1:n.90+1220A>G

Variant summary

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

The ENST00000784364.1(LINC02177):​n.90+1220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,114 control chromosomes in the GnomAD database, including 5,299 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 0.25 (5299 hom., cov: 32)
• Consequence: LINC02177 ENST00000784364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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

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
	LINC02177	ENST00000784364.1		n.90+1220A>G		intron	N/A
	LINC02177	ENST00000784365.1		n.85+1220A>G		intron	N/A
	LINC02177	ENST00000784366.1		n.69+1220A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38726 AN: 151996 Hom.: 5291 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.255 AC: 38774 AN: 152114 Hom.: 5299 Cov.: 32 AF XY: 0.259 AC XY: 19286 AN XY: 74358

African (AFR) AF: 0.182 AC: 7546 AN: 41496

American (AMR) AF: 0.258 AC: 3939 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2501 AN: 5168

South Asian (SAS) AF: 0.293 AC: 1409 AN: 4812

European-Finnish (FIN) AF: 0.315 AC: 3332 AN: 10582

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18282 AN: 68000

Other (OTH) AF: 0.249 AC: 525 AN: 2108

Alfa AF: 0.263 Hom.: 21956

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.95
DANN	Benign	0.19
PhyloP100		-0.31

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: rs8061903;

hg19: chr16-9382329;