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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747616.2	n.1639+1523T>G		intron_variant	Intron 3 of 5
LINC02641	XR_001747617.3	n.918+1523T>G		intron_variant	Intron 4 of 6
LINC02641	XR_001747618.2	n.896+1523T>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000662754.1	n.890+1523T>G		intron_variant	Intron 3 of 3
LINC02641	ENST00000812699.1	n.274-26610T>G		intron_variant	Intron 2 of 3
LINC02641	ENST00000812701.1	n.294-26610T>G		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs705169; hg19: chr10-125285443;