10-6348230-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC02649	ENST00000659311.1	n.622+3450G>C		intron_variant	Intron 4 of 4

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

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.744

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2387397; hg19: chr10-6390192;