10-6359663-C-T

Variant names:

• chr10-6359663-C-T
• rs4558075
• ENST00000783921.1:n.405+14883C>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+14883C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 151,484 control chromosomes in the GnomAD database, including 50,614 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 (50614 hom., cov: 30)
• Consequence: LINC02649 ENST00000783921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 8 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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+14883C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.817 AC: 123630 AN: 151372 Hom.: 50572 Cov.: 30

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.817 AC: 123724 AN: 151484 Hom.: 50614 Cov.: 30 AF XY: 0.820 AC XY: 60667 AN XY: 74002

African (AFR) AF: 0.771 AC: 31852 AN: 41320

American (AMR) AF: 0.875 AC: 13329 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2833 AN: 3466

East Asian (EAS) AF: 0.976 AC: 5052 AN: 5176

South Asian (SAS) AF: 0.864 AC: 4156 AN: 4812

European-Finnish (FIN) AF: 0.819 AC: 8566 AN: 10462

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

European-Non Finnish (NFE) AF: 0.816 AC: 55226 AN: 67718

Other (OTH) AF: 0.818 AC: 1720 AN: 2102

Alfa AF: 0.816 Hom.: 165383

Bravo AF: 0.818

Asia WGS AF: 0.907 AC: 3130 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.18
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs4558075; hg19: chr10-6401625;