10-130401217-T-A

Position:

• chr10-130401217-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02646	ENST00000648275.1	n.504-81664T>A		intron_variant, non_coding_transcript_variant

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;