rs12546080

Variant names:

• chr8-136048070-G-A
• rs12546080
• ENST00000502901.6:n.185+865G>A

Variant summary

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

The ENST00000502901.6(LINC02055):​n.185+865G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,990 control chromosomes in the GnomAD database, including 19,175 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 0.50 (19175 hom., cov: 32)
• Consequence: LINC02055 ENST00000502901.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969
• Publications: 4 publications found

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 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
LINC02055	ENST00000502901.6	n.185+865G>A		intron_variant	Intron 1 of 3	4
LINC02055	ENST00000523150.1	n.159+865G>A		intron_variant	Intron 1 of 4	5
LINC02055	ENST00000648077.2	n.112+865G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75415 AN: 151870 Hom.: 19163 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.496 AC: 75455 AN: 151990 Hom.: 19175 Cov.: 32 AF XY: 0.499 AC XY: 37090 AN XY: 74290

African (AFR) AF: 0.375 AC: 15559 AN: 41456

American (AMR) AF: 0.532 AC: 8122 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1638 AN: 3462

East Asian (EAS) AF: 0.686 AC: 3526 AN: 5138

South Asian (SAS) AF: 0.615 AC: 2961 AN: 4818

European-Finnish (FIN) AF: 0.561 AC: 5922 AN: 10564

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36098 AN: 67958

Other (OTH) AF: 0.499 AC: 1056 AN: 2116

Alfa AF: 0.516 Hom.: 3552

Bravo AF: 0.491

Asia WGS AF: 0.634 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.61
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs12546080; hg19: chr8-137060313;