rs11017221

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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.504-113080C>T		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0947

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.159

Alfa AF: 0.141 Hom.: 3081

Bravo AF: 0.140

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11017221; hg19: chr10-132168065;