10-130279480-A-T

Variant names:

• chr10-130279480-A-T
• rs318931
• ENST00000648275.1:n.503+65451A>T

Variant summary

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

The ENST00000648275.1(LINC02646):​n.503+65451A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,154 control chromosomes in the GnomAD database, including 18,410 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 0.48 (18410 hom., cov: 34)
• Consequence: LINC02646 ENST00000648275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.884
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 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.503+65451A>T		intron	N/A
	LINC02646	ENST00000739872.1		n.520-24599A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 73000 AN: 152036 Hom.: 18401 Cov.: 34

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.480 AC: 73022 AN: 152154 Hom.: 18410 Cov.: 34 AF XY: 0.474 AC XY: 35250 AN XY: 74390

African (AFR) AF: 0.340 AC: 14108 AN: 41502

American (AMR) AF: 0.496 AC: 7587 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1698 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1683 AN: 5180

South Asian (SAS) AF: 0.326 AC: 1573 AN: 4820

European-Finnish (FIN) AF: 0.528 AC: 5580 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39062 AN: 67998

Other (OTH) AF: 0.484 AC: 1023 AN: 2114

Alfa AF: 0.529 Hom.: 2712

Bravo AF: 0.477

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.50
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs318931; hg19: chr10-132077744;