rs6097080

Variant names:

• chr20-52699511-G-A
• rs6097080
• ENST00000656343.1:n.*39G>A

Variant summary

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

The ENST00000656343.1(LINC01524):​n.*39G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,170 control chromosomes in the GnomAD database, including 1,294 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 0.082 (1294 hom., cov: 32)
• Consequence: LINC01524 ENST00000656343.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 1 publications found

Genes affected

LINC01524 (HGNC:51228): (long intergenic non-protein coding RNA 1524)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000656343.1	n.*39G>A		downstream_gene_variant
LINC01524	ENST00000661770.1	n.*40G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12466 AN: 152052 Hom.: 1277 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0589

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0613

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

GnomAD4 genome AF: 0.0824 AC: 12534 AN: 152170 Hom.: 1294 Cov.: 32 AF XY: 0.0809 AC XY: 6022 AN XY: 74424

African (AFR) AF: 0.245 AC: 10149 AN: 41462

American (AMR) AF: 0.0480 AC: 734 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.0362 AC: 188 AN: 5188

South Asian (SAS) AF: 0.0590 AC: 284 AN: 4814

European-Finnish (FIN) AF: 0.0241 AC: 256 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0114 AC: 773 AN: 68022

Other (OTH) AF: 0.0611 AC: 129 AN: 2110

Alfa AF: 0.0333 Hom.: 262

Bravo AF: 0.0895

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.011
DANN	Benign	0.70
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6097080; hg19: chr20-51316050;