4-54368658-C-G

Variant names:

• chr4-54368658-C-G
• rs17690232
• ENST00000716476.1:n.637-7588C>G

Variant summary

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

The ENST00000716476.1(LINC02283):​n.637-7588C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,070 control chromosomes in the GnomAD database, including 1,794 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 0.14 (1794 hom., cov: 32)
• Consequence: LINC02283 ENST00000716476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 10 publications found

Genes affected

LINC02283 (HGNC:53200): (long intergenic non-protein coding RNA 2283)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716476.1. 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
	LINC02283	ENST00000716476.1		n.637-7588C>G		intron	N/A
	LINC02283	ENST00000801797.1		n.295-7588C>G		intron	N/A
	LINC02283	ENST00000801798.1		n.59-7588C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21574 AN: 151952 Hom.: 1794 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00502

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.142 AC: 21575 AN: 152070 Hom.: 1794 Cov.: 32 AF XY: 0.139 AC XY: 10337 AN XY: 74322

African (AFR) AF: 0.0771 AC: 3198 AN: 41490

American (AMR) AF: 0.124 AC: 1897 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3468

East Asian (EAS) AF: 0.00523 AC: 27 AN: 5166

South Asian (SAS) AF: 0.130 AC: 625 AN: 4816

European-Finnish (FIN) AF: 0.151 AC: 1595 AN: 10576

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13029 AN: 67950

Other (OTH) AF: 0.148 AC: 311 AN: 2108

Alfa AF: 0.165 Hom.: 1256

Bravo AF: 0.135

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.77
PhyloP100		-0.057

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: rs17690232;

hg19: chr4-55234825;