10-123462521-T-G

Variant names:

• chr10-123462521-T-G
• rs2282015
• ENST00000448347.5:n.746+13009T>G

Variant summary

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

The ENST00000448347.5(LINC02641):​n.746+13009T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,088 control chromosomes in the GnomAD database, including 12,053 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 0.39 (12053 hom., cov: 33)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 11 publications found

Genes affected

LINC02641 (HGNC:54125): (long intergenic non-protein coding RNA 2641)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448347.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02641	ENST00000448347.5	TSL:3	n.746+13009T>G		intron	N/A
	LINC02641	ENST00000448671.2	TSL:3	n.698+13009T>G		intron	N/A
	LINC02641	ENST00000655916.1		n.288+13009T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60012 AN: 151970 Hom.: 12040 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.395 AC: 60063 AN: 152088 Hom.: 12053 Cov.: 33 AF XY: 0.395 AC XY: 29354 AN XY: 74362

African (AFR) AF: 0.380 AC: 15767 AN: 41440

American (AMR) AF: 0.462 AC: 7061 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3466

East Asian (EAS) AF: 0.541 AC: 2801 AN: 5182

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4830

European-Finnish (FIN) AF: 0.363 AC: 3845 AN: 10584

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26274 AN: 67996

Other (OTH) AF: 0.432 AC: 909 AN: 2106

Alfa AF: 0.395 Hom.: 38470

Bravo AF: 0.408

Asia WGS AF: 0.398 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.73
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2282015; hg19: chr10-125222037;