10-123525927-T-G

Variant names:

• chr10-123525927-T-G
• rs705169
• ENST00000662754.1:n.890+1523T>G

Variant summary

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

The ENST00000662754.1(LINC02641):​n.890+1523T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,012 control chromosomes in the GnomAD database, including 21,805 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 0.53 (21805 hom., cov: 32)
• Consequence: LINC02641 ENST00000662754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662754.1. 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	ENST00000662754.1		n.890+1523T>G		intron	N/A
	LINC02641	ENST00000812699.1		n.274-26610T>G		intron	N/A
	LINC02641	ENST00000812701.1		n.294-26610T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80752 AN: 151894 Hom.: 21772 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.532 AC: 80836 AN: 152012 Hom.: 21805 Cov.: 32 AF XY: 0.530 AC XY: 39402 AN XY: 74282

African (AFR) AF: 0.594 AC: 24613 AN: 41436

American (AMR) AF: 0.533 AC: 8148 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3657 AN: 5172

South Asian (SAS) AF: 0.547 AC: 2629 AN: 4808

European-Finnish (FIN) AF: 0.468 AC: 4943 AN: 10560

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33587 AN: 67970

Other (OTH) AF: 0.520 AC: 1097 AN: 2110

Alfa AF: 0.509 Hom.: 85456

Bravo AF: 0.546

Asia WGS AF: 0.599 AC: 2083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		-0.085

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs705169;

hg19: chr10-125285443;