chr4-6657957-C-T

Variant names:

• chr4-6657957-C-T
• rs4689495
• ENST00000777168.1:n.577G>A

Variant summary

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

The ENST00000777168.1(LINC02482):​n.577G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,150 control chromosomes in the GnomAD database, including 32,852 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 0.66 (32852 hom., cov: 33)
• Consequence: LINC02482 ENST00000777168.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 5 publications found

Genes affected

LINC02482 (HGNC:53458): (long intergenic non-protein coding RNA 2482)

LOC124900840 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777168.1. 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
	LINC02482	ENST00000777168.1		n.577G>A		non_coding_transcript_exon	Exon 4 of 4
	LINC02482	ENST00000777171.1		n.520G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC02482	ENST00000647523.2		n.429+1495G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99566 AN: 152032 Hom.: 32813 Cov.: 33

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.655 AC: 99666 AN: 152150 Hom.: 32852 Cov.: 33 AF XY: 0.660 AC XY: 49067 AN XY: 74370

African (AFR) AF: 0.703 AC: 29201 AN: 41512

American (AMR) AF: 0.633 AC: 9682 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2725 AN: 5158

South Asian (SAS) AF: 0.715 AC: 3447 AN: 4822

European-Finnish (FIN) AF: 0.730 AC: 7728 AN: 10592

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42920 AN: 67988

Other (OTH) AF: 0.625 AC: 1322 AN: 2114

Alfa AF: 0.636 Hom.: 17374

Bravo AF: 0.649

Asia WGS AF: 0.665 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.61
PhyloP100		-0.38

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: rs4689495;

hg19: chr4-6659684;