6-92659937-G-T

Variant names:

• chr6-92659937-G-T
• rs6918777
• NR_189297.1:n.506-26339C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_189297.1(LINC02531):​n.506-26339C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,954 control chromosomes in the GnomAD database, including 16,217 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 0.46 (16217 hom., cov: 32)
• Consequence: LINC02531 NR_189297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02531	NR_189297.1	n.506-26339C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69246 AN: 151836 Hom.: 16183 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.456 AC: 69337 AN: 151954 Hom.: 16217 Cov.: 32 AF XY: 0.459 AC XY: 34073 AN XY: 74270

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.482

Alfa AF: 0.446 Hom.: 30622

Bravo AF: 0.477

Asia WGS AF: 0.576 AC: 1996 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6918777; hg19: chr6-93369655; COSMIC: COSV60247149;