rs6716455

Variant names:

• chr2-150269889-G-A
• rs6716455
• ENST00000437118.1:n.261-31084G>A

Variant summary

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

The ENST00000437118.1(LINC01818):​n.261-31084G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,198 control chromosomes in the GnomAD database, including 1,268 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 0.12 (1268 hom., cov: 33)
• Consequence: LINC01818 ENST00000437118.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 9 publications found

Genes affected

LINC01818 (HGNC:52623): (long intergenic non-protein coding RNA 1818)

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 (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437118.1. 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
	LINC01818	NR_187171.1		n.230+55477G>A		intron	N/A
	LINC01818	NR_187172.1		n.230+55477G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01818	ENST00000437118.1	TSL:2	n.261-31084G>A		intron	N/A
	LINC01818	ENST00000659082.1		n.245+55477G>A		intron	N/A
	LINC01818	ENST00000665690.1		n.200+55477G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17765 AN: 152080 Hom.: 1268 Cov.: 33

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.117 AC: 17765 AN: 152198 Hom.: 1268 Cov.: 33 AF XY: 0.118 AC XY: 8784 AN XY: 74380

African (AFR) AF: 0.0385 AC: 1600 AN: 41534

American (AMR) AF: 0.143 AC: 2186 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 685 AN: 3470

East Asian (EAS) AF: 0.193 AC: 997 AN: 5166

South Asian (SAS) AF: 0.140 AC: 675 AN: 4830

European-Finnish (FIN) AF: 0.133 AC: 1405 AN: 10568

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9738 AN: 68016

Other (OTH) AF: 0.136 AC: 288 AN: 2116

Alfa AF: 0.139 Hom.: 3895

Bravo AF: 0.113

Asia WGS AF: 0.146 AC: 508 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.96
DANN	Benign	0.69
PhyloP100		-0.50

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: rs6716455;

hg19: chr2-151126403;