rs827640

Variant names:

• chr10-8946048-C-T
• rs827640
• ENST00000837048.1:n.849+15684C>T

Variant summary

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

The ENST00000837048.1(LINC02676):​n.849+15684C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,572 control chromosomes in the GnomAD database, including 11,917 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 0.39 (11917 hom., cov: 31)
• Consequence: LINC02676 ENST00000837048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 3 publications found

Genes affected

LINC02676 (HGNC:54170): (long intergenic non-protein coding RNA 2676)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 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
LINC02676	ENST00000837048.1	n.849+15684C>T		intron_variant	Intron 2 of 4
LINC02676	ENST00000837049.1	n.784+1882C>T		intron_variant	Intron 2 of 4
LINC02676	ENST00000837050.1	n.704-20495C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58654 AN: 151454 Hom.: 11895 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.387 AC: 58717 AN: 151572 Hom.: 11917 Cov.: 31 AF XY: 0.387 AC XY: 28642 AN XY: 74034

African (AFR) AF: 0.401 AC: 16578 AN: 41360

American (AMR) AF: 0.481 AC: 7296 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1249 AN: 3462

East Asian (EAS) AF: 0.669 AC: 3447 AN: 5150

South Asian (SAS) AF: 0.469 AC: 2256 AN: 4810

European-Finnish (FIN) AF: 0.243 AC: 2552 AN: 10500

Middle Eastern (MID) AF: 0.455 AC: 132 AN: 290

European-Non Finnish (NFE) AF: 0.355 AC: 24081 AN: 67812

Other (OTH) AF: 0.436 AC: 916 AN: 2102

Alfa AF: 0.360 Hom.: 4404

Bravo AF: 0.409

Asia WGS AF: 0.562 AC: 1948 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs827640; hg19: chr10-8988011;