chr6-92639124-G-A

Variant names:

• chr6-92639124-G-A
• rs10498982
• ENST00000404689.3:n.594-5523C>T

Variant summary

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

The NR_189297.1(LINC02531):​n.506-5526C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,920 control chromosomes in the GnomAD database, including 9,234 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 0.33 (9234 hom., cov: 32)
• Consequence: LINC02531 NR_189297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 5 publications found

Genes affected

LINC02531 (HGNC:53557): (long intergenic non-protein coding RNA 2531)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_189297.1. 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
	LINC02531	NR_189297.1		n.506-5526C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02531	ENST00000404689.3	TSL:5	n.594-5523C>T		intron	N/A
	LINC02531	ENST00000799047.1		n.463-5526C>T		intron	N/A
	LINC02531	ENST00000799048.1		n.149-5526C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49824 AN: 151802 Hom.: 9236 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.328 AC: 49820 AN: 151920 Hom.: 9234 Cov.: 32 AF XY: 0.324 AC XY: 24056 AN XY: 74252

African (AFR) AF: 0.164 AC: 6817 AN: 41474

American (AMR) AF: 0.269 AC: 4112 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1281 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1270 AN: 5146

South Asian (SAS) AF: 0.322 AC: 1548 AN: 4810

European-Finnish (FIN) AF: 0.390 AC: 4102 AN: 10524

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29466 AN: 67928

Other (OTH) AF: 0.340 AC: 715 AN: 2106

Alfa AF: 0.393 Hom.: 22935

Bravo AF: 0.310

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		0.60

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: rs10498982;

hg19: chr6-93348842;