6-137923806-C-T

Variant names:

• chr6-137923806-C-T
• rs1545092
• ENST00000752757.1:n.68+218C>T

Variant summary

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

The ENST00000752757.1(LINC02865):​n.68+218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,138 control chromosomes in the GnomAD database, including 42,592 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 0.74 (42592 hom., cov: 31)
• Consequence: LINC02865 ENST00000752757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 12 publications found

Genes affected

LINC02865 (HGNC:54516): (long intergenic non-protein coding RNA 2865)

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 = 0.96 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
LINC02865	ENST00000752757.1	n.68+218C>T		intron_variant	Intron 1 of 3
LINC02865	ENST00000752758.1	n.66+218C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111723 AN: 152020 Hom.: 42533 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.735 AC: 111848 AN: 152138 Hom.: 42592 Cov.: 31 AF XY: 0.739 AC XY: 54989 AN XY: 74372

African (AFR) AF: 0.927 AC: 38515 AN: 41532

American (AMR) AF: 0.728 AC: 11136 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2428 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5088 AN: 5178

South Asian (SAS) AF: 0.778 AC: 3750 AN: 4822

European-Finnish (FIN) AF: 0.661 AC: 6979 AN: 10566

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41655 AN: 67970

Other (OTH) AF: 0.724 AC: 1527 AN: 2108

Alfa AF: 0.661 Hom.: 44844

Bravo AF: 0.747

Asia WGS AF: 0.873 AC: 3031 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1545092; hg19: chr6-138244943;