chr5-92897017-A-C

Variant names:

• chr5-92897017-A-C
• rs1988145
• ENST00000766746.1:n.241-8422T>G

Variant summary

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

The ENST00000766746.1(LINC02058):​n.241-8422T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,998 control chromosomes in the GnomAD database, including 41,778 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 0.74 (41778 hom., cov: 33)
• Consequence: LINC02058 ENST00000766746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 4 publications found

Genes affected

LINC02058 (HGNC:52901): (long intergenic non-protein coding RNA 2058)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766746.1. 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
	LINC02058	ENST00000766746.1		n.241-8422T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111896 AN: 151880 Hom.: 41726 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.737 AC: 112006 AN: 151998 Hom.: 41778 Cov.: 33 AF XY: 0.736 AC XY: 54654 AN XY: 74270

African (AFR) AF: 0.854 AC: 35448 AN: 41500

American (AMR) AF: 0.768 AC: 11718 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2271 AN: 3472

East Asian (EAS) AF: 0.847 AC: 4367 AN: 5158

South Asian (SAS) AF: 0.709 AC: 3417 AN: 4818

European-Finnish (FIN) AF: 0.661 AC: 6988 AN: 10566

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45433 AN: 67920

Other (OTH) AF: 0.719 AC: 1517 AN: 2110

Alfa AF: 0.674 Hom.: 51383

Bravo AF: 0.754

Asia WGS AF: 0.784 AC: 2723 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		-0.029

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: rs1988145;

hg19: chr5-92232724;

COSMIC: COSV60167871;