rs9450270

Variant names:

• chr6-85405048-A-G
• rs9450270
• ENST00000840424.1:n.-137T>C

Variant summary

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

The ENST00000840424.1(LINC02535):​n.-137T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,030 control chromosomes in the GnomAD database, including 3,497 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 0.18 (3497 hom., cov: 32)
• Consequence: LINC02535 ENST00000840424.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 6 publications found

Genes affected

LINC02535 (HGNC:53569): (long intergenic non-protein coding RNA 2535)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02535	NR_134633.1	n.-246T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02535	ENST00000840424.1	n.-137T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27655 AN: 151912 Hom.: 3489 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.182 AC: 27697 AN: 152030 Hom.: 3497 Cov.: 32 AF XY: 0.179 AC XY: 13302 AN XY: 74342

African (AFR) AF: 0.359 AC: 14841 AN: 41390

American (AMR) AF: 0.117 AC: 1793 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3466

East Asian (EAS) AF: 0.0565 AC: 292 AN: 5168

South Asian (SAS) AF: 0.141 AC: 681 AN: 4826

European-Finnish (FIN) AF: 0.107 AC: 1130 AN: 10596

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.117 AC: 7952 AN: 67982

Other (OTH) AF: 0.162 AC: 341 AN: 2110

Alfa AF: 0.137 Hom.: 2247

Bravo AF: 0.188

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs9450270; hg19: chr6-86114766;