6-113906148-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027060.1(LINC02880):n.358+1404C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,172 control chromosomes in the GnomAD database, including 29,251 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 0.61 (29251 hom., cov: 33)
• Consequence: LINC02880 NR_027060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

LINC02880 (HGNC:54660): (long intergenic non-protein coding RNA 2880)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02880	NR_027060.1	n.358+1404C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02880	ENST00000314481.3	n.607+1404C>T		intron_variant, non_coding_transcript_variant		2
LINC02880	ENST00000658538.1	n.613+1404C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92611 AN: 152054 Hom.: 29215 Cov.: 33

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.609 AC: 92697 AN: 152172 Hom.: 29251 Cov.: 33 AF XY: 0.613 AC XY: 45621 AN XY: 74388

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.586

Alfa AF: 0.475 Hom.: 2125

Bravo AF: 0.602

Asia WGS AF: 0.758 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.91
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs352095; hg19: chr6-114227312;