chr10-6360717-C-G

Variant names:

• chr10-6360717-C-G
• rs10752291
• ENST00000783921.1:n.405+15937C>G

Variant summary

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

The ENST00000783921.1(LINC02649):​n.405+15937C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,120 control chromosomes in the GnomAD database, including 50,700 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 (50700 hom., cov: 32)
• Consequence: LINC02649 ENST00000783921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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+15937C>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123976 AN: 152000 Hom.: 50657 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.816 AC: 124075 AN: 152120 Hom.: 50700 Cov.: 32 AF XY: 0.819 AC XY: 60883 AN XY: 74352

African (AFR) AF: 0.768 AC: 31857 AN: 41490

American (AMR) AF: 0.875 AC: 13389 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2837 AN: 3468

East Asian (EAS) AF: 0.976 AC: 5064 AN: 5190

South Asian (SAS) AF: 0.864 AC: 4168 AN: 4824

European-Finnish (FIN) AF: 0.817 AC: 8608 AN: 10542

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

European-Non Finnish (NFE) AF: 0.815 AC: 55434 AN: 67996

Other (OTH) AF: 0.817 AC: 1726 AN: 2112

Alfa AF: 0.775 Hom.: 2678

Bravo AF: 0.817

Asia WGS AF: 0.908 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10752291; hg19: chr10-6402679;