6-92659937-G-T

Variant names:

• chr6-92659937-G-T
• rs6918777
• ENST00000404689.3:n.594-26336C>A

Variant summary

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

The ENST00000404689.3(LINC02531):​n.594-26336C>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 ENST00000404689.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000404689.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02531	NR_189297.1		n.506-26339C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02531	ENST00000404689.3	TSL:5	n.594-26336C>A		intron	N/A
	LINC02531	ENST00000799047.1		n.463-26339C>A		intron	N/A
	LINC02531	ENST00000799048.1		n.149-26339C>A		intron	N/A

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

African (AFR) AF: 0.422 AC: 17471 AN: 41422

American (AMR) AF: 0.609 AC: 9284 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1618 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3611 AN: 5158

South Asian (SAS) AF: 0.460 AC: 2221 AN: 4824

European-Finnish (FIN) AF: 0.394 AC: 4151 AN: 10544

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29426 AN: 67972

Other (OTH) AF: 0.482 AC: 1019 AN: 2114

Alfa AF: 0.448 Hom.: 63281

Bravo AF: 0.477

Asia WGS AF: 0.576 AC: 1996 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.22
PhyloP100		-0.34

Splicing

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

Other links and lift over

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