ENST00000488425.1:n.310-9287G>T

Variant names:

• chr3-127334018-C-A
• rs2358551
• ENST00000488425.1:n.310-9287G>T

Variant summary

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

The ENST00000488425.1(LINC02016):​n.310-9287G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,004 control chromosomes in the GnomAD database, including 4,144 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 0.23 (4144 hom., cov: 32)
• Consequence: LINC02016 ENST00000488425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 1 publications found

Genes affected

LINC02016 (HGNC:52851): (long intergenic non-protein coding RNA 2016)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488425.1. 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
	LINC02016	NR_110147.1		n.310-9287G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02016	ENST00000488425.1	TSL:1	n.310-9287G>T		intron	N/A
	LINC02016	ENST00000654968.1		n.170-9287G>T		intron	N/A
	LINC02016	ENST00000663573.2		n.141+4201G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34508 AN: 151886 Hom.: 4141 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.227 AC: 34535 AN: 152004 Hom.: 4144 Cov.: 32 AF XY: 0.222 AC XY: 16457 AN XY: 74292

African (AFR) AF: 0.246 AC: 10215 AN: 41458

American (AMR) AF: 0.186 AC: 2841 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5176

South Asian (SAS) AF: 0.136 AC: 654 AN: 4814

European-Finnish (FIN) AF: 0.210 AC: 2208 AN: 10536

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16668 AN: 67964

Other (OTH) AF: 0.275 AC: 580 AN: 2106

Alfa AF: 0.123 Hom.: 225

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		-0.13

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: rs2358551;

hg19: chr3-127052861;