rs12198063

Positions:

• chr6-76581082-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02540	NR_149101.1	n.216+5366T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02540	ENST00000455554.2	n.216+5366T>C		intron_variant		3
LINC02540	ENST00000653622.1	n.153+5366T>C		intron_variant

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

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0675

Gnomad4 ASJ AF: 0.0543

Gnomad4 EAS AF: 0.0429

Gnomad4 SAS AF: 0.0817

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0944 Hom.: 972

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12198063; hg19: chr6-77290799;