6-113906148-C-T

Variant names:

• chr6-113906148-C-T
• rs352095
• ENST00000314481.4:n.625+1404C>T

Variant summary

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

The ENST00000314481.4(LINC02880):​n.625+1404C>T variant causes a intron 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 ENST00000314481.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000314481.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02880	NR_027060.1		n.358+1404C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02880	ENST00000314481.4	TSL:2	n.625+1404C>T		intron	N/A
	LINC02880	ENST00000658538.1		n.613+1404C>T		intron	N/A
	LINC02880	ENST00000793169.1		n.660+1404C>T		intron	N/A

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

African (AFR) AF: 0.758 AC: 31458 AN: 41526

American (AMR) AF: 0.489 AC: 7481 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4298 AN: 5188

South Asian (SAS) AF: 0.669 AC: 3226 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6581 AN: 10566

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35680 AN: 67988

Other (OTH) AF: 0.586 AC: 1241 AN: 2116

Alfa AF: 0.489 Hom.: 2346

Bravo AF: 0.602

Asia WGS AF: 0.758 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.57
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs352095; hg19: chr6-114227312;