10-6360779-G-T

Variant names:

• chr10-6360779-G-T
• rs10796045
• ENST00000783921.1:n.405+15999G>T

Variant summary

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

The ENST00000783921.1(LINC02649):​n.405+15999G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,074 control chromosomes in the GnomAD database, including 48,080 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 0.79 (48080 hom., cov: 32)
• Consequence: LINC02649 ENST00000783921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 12 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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	ENST00000783921.1	n.405+15999G>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120694 AN: 151956 Hom.: 48060 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.794 AC: 120762 AN: 152074 Hom.: 48080 Cov.: 32 AF XY: 0.796 AC XY: 59156 AN XY: 74326

African (AFR) AF: 0.715 AC: 29656 AN: 41452

American (AMR) AF: 0.857 AC: 13111 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2835 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4564 AN: 5184

South Asian (SAS) AF: 0.809 AC: 3900 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8618 AN: 10540

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55398 AN: 67994

Other (OTH) AF: 0.800 AC: 1689 AN: 2110

Alfa AF: 0.807 Hom.: 77053

Bravo AF: 0.793

Asia WGS AF: 0.842 AC: 2932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.091
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs10796045; hg19: chr10-6402741;