chr10-6361088-G-C

Variant names:

• chr10-6361088-G-C
• rs2146900
• ENST00000783921.1:n.405+16308G>C

Variant summary

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

The ENST00000783921.1(LINC02649):​n.405+16308G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 151,946 control chromosomes in the GnomAD database, including 51,347 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 0.82 (51347 hom., cov: 29)
• Consequence: LINC02649 ENST00000783921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 4 publications found

Genes affected

LINC02649 (HGNC:54134): (long intergenic non-protein coding RNA 2649)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783921.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02649	ENST00000783921.1		n.405+16308G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124680 AN: 151828 Hom.: 51302 Cov.: 29

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.821 AC: 124780 AN: 151946 Hom.: 51347 Cov.: 29 AF XY: 0.824 AC XY: 61207 AN XY: 74248

African (AFR) AF: 0.774 AC: 32064 AN: 41404

American (AMR) AF: 0.882 AC: 13479 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2842 AN: 3472

East Asian (EAS) AF: 0.975 AC: 5049 AN: 5176

South Asian (SAS) AF: 0.858 AC: 4134 AN: 4818

European-Finnish (FIN) AF: 0.823 AC: 8644 AN: 10502

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55832 AN: 67978

Other (OTH) AF: 0.821 AC: 1728 AN: 2104

Alfa AF: 0.771 Hom.: 2312

Bravo AF: 0.823

Asia WGS AF: 0.908 AC: 3158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2146900; hg19: chr10-6403050;