chr10-130401217-T-A

Variant names:

• chr10-130401217-T-A
• rs11017236
• ENST00000648275.1:n.504-81664T>A

Variant summary

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

The ENST00000648275.1(LINC02646):​n.504-81664T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,154 control chromosomes in the GnomAD database, including 8,311 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 0.28 (8311 hom., cov: 33)
• Consequence: LINC02646 ENST00000648275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 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.504-81664T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42437 AN: 152036 Hom.: 8286 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.279 AC: 42506 AN: 152154 Hom.: 8311 Cov.: 33 AF XY: 0.277 AC XY: 20604 AN XY: 74394

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.251

Alfa AF: 0.215 Hom.: 670

Bravo AF: 0.296

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11017236; hg19: chr10-132199481;