10-6362738-T-G

Variant names:

• chr10-6362738-T-G
• rs1570527
• ENST00000783921.1:n.405+17958T>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+17958T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,120 control chromosomes in the GnomAD database, including 51,362 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 (51362 hom., cov: 31)
• Consequence: LINC02649 ENST00000783921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 7 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=-0.97).
• 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+17958T>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124746 AN: 152002 Hom.: 51321 Cov.: 31

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.821 AC: 124842 AN: 152120 Hom.: 51362 Cov.: 31 AF XY: 0.824 AC XY: 61276 AN XY: 74352

African (AFR) AF: 0.770 AC: 31972 AN: 41498

American (AMR) AF: 0.882 AC: 13474 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2849 AN: 3470

East Asian (EAS) AF: 0.976 AC: 5058 AN: 5182

South Asian (SAS) AF: 0.873 AC: 4208 AN: 4820

European-Finnish (FIN) AF: 0.821 AC: 8685 AN: 10576

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

European-Non Finnish (NFE) AF: 0.822 AC: 55855 AN: 67980

Other (OTH) AF: 0.822 AC: 1731 AN: 2106

Alfa AF: 0.822 Hom.: 36516

Bravo AF: 0.822

Asia WGS AF: 0.911 AC: 3168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1570527; hg19: chr10-6404700;