chr10-130341244-C-T

Variant names:

• chr10-130341244-C-T
• rs447363
• ENST00000648275.1:n.503+127215C>T

Variant summary

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

The ENST00000648275.1(LINC02646):​n.503+127215C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,094 control chromosomes in the GnomAD database, including 15,893 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 0.45 (15893 hom., cov: 33)
• Consequence: LINC02646 ENST00000648275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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.503+127215C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67838 AN: 151976 Hom.: 15868 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.446 AC: 67908 AN: 152094 Hom.: 15893 Cov.: 33 AF XY: 0.451 AC XY: 33534 AN XY: 74324

African (AFR) AF: 0.319 AC: 13224 AN: 41494

American (AMR) AF: 0.477 AC: 7300 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1681 AN: 3466

East Asian (EAS) AF: 0.696 AC: 3596 AN: 5168

South Asian (SAS) AF: 0.609 AC: 2938 AN: 4826

European-Finnish (FIN) AF: 0.484 AC: 5112 AN: 10570

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32531 AN: 67970

Other (OTH) AF: 0.439 AC: 926 AN: 2108

Alfa AF: 0.470 Hom.: 61161

Bravo AF: 0.438

Asia WGS AF: 0.614 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.93
PhyloP100		-0.22

Splicing

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

Publications

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Other links and lift over

dbSNP: rs447363; hg19: chr10-132139508;