10-130257225-G-T

Variant names:

• chr10-130257225-G-T
• rs913628
• ENST00000648275.1:n.503+43196G>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+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
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648275.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02646	ENST00000648275.1		n.503+43196G>T		intron	N/A
	LINC02646	ENST00000739872.1		n.519+43196G>T		intron	N/A

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

African (AFR) AF: 0.427 AC: 17679 AN: 41430

American (AMR) AF: 0.313 AC: 4787 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1236 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1930 AN: 5162

South Asian (SAS) AF: 0.427 AC: 2059 AN: 4824

European-Finnish (FIN) AF: 0.303 AC: 3204 AN: 10578

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16812 AN: 67982

Other (OTH) AF: 0.314 AC: 662 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.74
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs913628; hg19: chr10-132055489;