rs11017221

chr10-130369801-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02646	ENST00000648275.1	n.504-113080C>T		intron_variant, non_coding_transcript_variant

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;