rs913628

Variant names:

• chr10-130257225-G-T
• rs913628
• ENST00000648275.1:n.503+43196G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648275.1(LINC02646):​n.503+43196G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,046 control chromosomes in the GnomAD database, including 8,167 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 0.32 (8167 hom., cov: 33)
• Consequence: LINC02646 ENST00000648275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 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+43196G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48578 AN: 151928 Hom.: 8154 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.320 AC: 48629 AN: 152046 Hom.: 8167 Cov.: 33 AF XY: 0.326 AC XY: 24226 AN XY: 74312

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.314

Alfa AF: 0.290 Hom.: 1093

Bravo AF: 0.323

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs913628; hg19: chr10-132055489;