10-6348230-G-C

Variant names:

• chr10-6348230-G-C
• rs2387397
• ENST00000659311.1:n.622+3450G>C

Variant summary

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

The ENST00000659311.1(LINC02649):​n.622+3450G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,962 control chromosomes in the GnomAD database, including 42,781 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 0.75 (42781 hom., cov: 30)
• Consequence: LINC02649 ENST00000659311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 22 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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659311.1. 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	ENST00000659311.1		n.622+3450G>C		intron	N/A
	LINC02649	ENST00000783921.1		n.405+3450G>C		intron	N/A
	LINC02649	ENST00000783922.1		n.422+3450G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113284 AN: 151844 Hom.: 42746 Cov.: 30

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.746 AC: 113375 AN: 151962 Hom.: 42781 Cov.: 30 AF XY: 0.752 AC XY: 55841 AN XY: 74282

African (AFR) AF: 0.622 AC: 25733 AN: 41388

American (AMR) AF: 0.816 AC: 12476 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2673 AN: 3468

East Asian (EAS) AF: 0.888 AC: 4592 AN: 5170

South Asian (SAS) AF: 0.822 AC: 3955 AN: 4812

European-Finnish (FIN) AF: 0.811 AC: 8558 AN: 10556

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52851 AN: 67964

Other (OTH) AF: 0.744 AC: 1571 AN: 2112

Alfa AF: 0.755 Hom.: 5128

Bravo AF: 0.738

Asia WGS AF: 0.828 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	18
DANN	Benign	0.63
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs2387397; hg19: chr10-6390192;