10-8968661-A-G

Variant names:

• chr10-8968661-A-G
• rs827637
• ENST00000837048.1:n.1079+135A>G

Variant summary

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

The ENST00000837048.1(LINC02676):​n.1079+135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,914 control chromosomes in the GnomAD database, including 20,433 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 0.51 (20433 hom., cov: 32)
• Consequence: LINC02676 ENST00000837048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837048.1. 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
	LINC02676	ENST00000837048.1		n.1079+135A>G		intron	N/A
	LINC02676	ENST00000837049.1		n.1014+135A>G		intron	N/A
	LINC02676	ENST00000837050.1		n.933+135A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77978 AN: 151798 Hom.: 20422 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.514 AC: 78022 AN: 151914 Hom.: 20433 Cov.: 32 AF XY: 0.512 AC XY: 37981 AN XY: 74234

African (AFR) AF: 0.475 AC: 19659 AN: 41382

American (AMR) AF: 0.446 AC: 6793 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1645 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1569 AN: 5166

South Asian (SAS) AF: 0.479 AC: 2307 AN: 4812

European-Finnish (FIN) AF: 0.636 AC: 6715 AN: 10558

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.554 AC: 37662 AN: 67966

Other (OTH) AF: 0.513 AC: 1084 AN: 2114

Alfa AF: 0.534 Hom.: 92966

Bravo AF: 0.498

Asia WGS AF: 0.407 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.50
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs827637; hg19: chr10-9010624;