rs12198063

Variant names:

• chr6-76581082-A-G
• rs12198063
• ENST00000455554.2:n.216+5366T>C

Variant summary

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

The ENST00000455554.2(LINC02540):​n.216+5366T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 151,666 control chromosomes in the GnomAD database, including 619 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 0.079 (619 hom., cov: 32)
• Consequence: LINC02540 ENST00000455554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 2 publications found

Genes affected

LINC02540 (HGNC:53573): (long intergenic non-protein coding RNA 2540)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02540	NR_149101.1	n.216+5366T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02540	ENST00000455554.2	n.216+5366T>C		intron_variant	Intron 2 of 2	3
LINC02540	ENST00000653622.1	n.153+5366T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11940 AN: 151548 Hom.: 620 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.0543

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0787 AC: 11929 AN: 151666 Hom.: 619 Cov.: 32 AF XY: 0.0784 AC XY: 5812 AN XY: 74092

African (AFR) AF: 0.0298 AC: 1237 AN: 41484

American (AMR) AF: 0.0675 AC: 1024 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0543 AC: 187 AN: 3444

East Asian (EAS) AF: 0.0429 AC: 220 AN: 5134

South Asian (SAS) AF: 0.0817 AC: 394 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1457 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7216 AN: 67706

Other (OTH) AF: 0.0762 AC: 160 AN: 2100

Alfa AF: 0.0896 Hom.: 1230

Bravo AF: 0.0713

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12198063; hg19: chr6-77290799;