4-117360214-G-A

Variant names:

• chr4-117360214-G-A
• rs11723116
• ENST00000416680.1:n.76+350C>T

Variant summary

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

The ENST00000416680.1(LINC02262):​n.76+350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,896 control chromosomes in the GnomAD database, including 2,987 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 0.19 (2987 hom., cov: 32)
• Consequence: LINC02262 ENST00000416680.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 3 publications found

Genes affected

LINC02262 (HGNC:53174): (long intergenic non-protein coding RNA 2262)

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 = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416680.1. 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
	LINC02262	NR_147151.1		n.76+350C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02262	ENST00000416680.1	TSL:3	n.76+350C>T		intron	N/A
	LINC02262	ENST00000653017.1		n.112+330C>T		intron	N/A
	LINC02262	ENST00000657433.1		n.89+330C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28875 AN: 151780 Hom.: 2983 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.190 AC: 28887 AN: 151896 Hom.: 2987 Cov.: 32 AF XY: 0.192 AC XY: 14279 AN XY: 74180

African (AFR) AF: 0.148 AC: 6137 AN: 41454

American (AMR) AF: 0.148 AC: 2263 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2150 AN: 5118

South Asian (SAS) AF: 0.246 AC: 1183 AN: 4816

European-Finnish (FIN) AF: 0.238 AC: 2512 AN: 10534

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13088 AN: 67944

Other (OTH) AF: 0.223 AC: 470 AN: 2108

Alfa AF: 0.192 Hom.: 12431

Bravo AF: 0.181

Asia WGS AF: 0.325 AC: 1126 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.34
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs11723116; hg19: chr4-118281370;