10-130351311-A-G

Variant names:

• chr10-130351311-A-G
• rs3858304
• ENST00000648275.1:n.504-131570A>G

Variant summary

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

The ENST00000648275.1(LINC02646):​n.504-131570A>G 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 151,544 control chromosomes in the GnomAD database, including 47,654 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 (47654 hom., cov: 30)
• Consequence: LINC02646 ENST00000648275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 3 publications found

Genes affected

LINC02646 (HGNC:54130): (long intergenic non-protein coding RNA 2646)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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
LINC02646	ENST00000648275.1	n.504-131570A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120185 AN: 151422 Hom.: 47608 Cov.: 30

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.794 AC: 120287 AN: 151544 Hom.: 47654 Cov.: 30 AF XY: 0.794 AC XY: 58793 AN XY: 74020

African (AFR) AF: 0.851 AC: 35211 AN: 41372

American (AMR) AF: 0.788 AC: 12012 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2741 AN: 3464

East Asian (EAS) AF: 0.817 AC: 4168 AN: 5104

South Asian (SAS) AF: 0.749 AC: 3568 AN: 4764

European-Finnish (FIN) AF: 0.795 AC: 8328 AN: 10480

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51669 AN: 67822

Other (OTH) AF: 0.791 AC: 1664 AN: 2104

Alfa AF: 0.778 Hom.: 61521

Bravo AF: 0.796

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.77
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs3858304; hg19: chr10-132149575;