rs4895501

Variant names:

• chr6-137966423-C-T
• rs4895501
• ENST00000417800.1:n.102-5820C>T

Variant summary

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

The ENST00000417800.1(LINC02865):​n.102-5820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,874 control chromosomes in the GnomAD database, including 15,068 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 0.44 (15068 hom., cov: 31)
• Consequence: LINC02865 ENST00000417800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 6 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=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417800.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02865	ENST00000417800.1	TSL:2	n.102-5820C>T		intron	N/A
	LINC02865	ENST00000752757.1		n.168-5820C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66470 AN: 151756 Hom.: 15044 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.438 AC: 66539 AN: 151874 Hom.: 15068 Cov.: 31 AF XY: 0.447 AC XY: 33148 AN XY: 74204

African (AFR) AF: 0.450 AC: 18619 AN: 41356

American (AMR) AF: 0.495 AC: 7565 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1843 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3261 AN: 5172

South Asian (SAS) AF: 0.592 AC: 2848 AN: 4808

European-Finnish (FIN) AF: 0.462 AC: 4858 AN: 10526

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26270 AN: 67942

Other (OTH) AF: 0.429 AC: 905 AN: 2110

Alfa AF: 0.395 Hom.: 11588

Bravo AF: 0.437

Asia WGS AF: 0.595 AC: 2069 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.29
DANN	Benign	0.54
PhyloP100		-2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4895501;

hg19: chr6-138287560;