chr10-130369801-C-T

Variant names:

• chr10-130369801-C-T
• rs11017221
• ENST00000648275.1:n.504-113080C>T

Variant summary

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

The ENST00000648275.1(LINC02646):​n.504-113080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,190 control chromosomes in the GnomAD database, including 1,423 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 0.13 (1423 hom., cov: 33)
• Consequence: LINC02646 ENST00000648275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 7 publications found

Genes affected

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

ENSG00000294189 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02646	ENST00000648275.1		n.504-113080C>T		intron	N/A
	ENSG00000294189	ENST00000721801.1		n.79+557C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20447 AN: 152072 Hom.: 1422 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0947

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.134 AC: 20450 AN: 152190 Hom.: 1423 Cov.: 33 AF XY: 0.130 AC XY: 9699 AN XY: 74388

African (AFR) AF: 0.138 AC: 5733 AN: 41520

American (AMR) AF: 0.130 AC: 1989 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3470

East Asian (EAS) AF: 0.139 AC: 713 AN: 5144

South Asian (SAS) AF: 0.104 AC: 504 AN: 4826

European-Finnish (FIN) AF: 0.0947 AC: 1005 AN: 10610

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9559 AN: 68002

Other (OTH) AF: 0.159 AC: 336 AN: 2114

Alfa AF: 0.139 Hom.: 6351

Bravo AF: 0.140

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.97
DANN	Benign	0.78
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11017221; hg19: chr10-132168065;