10-123526421-A-C

Variant names:

• chr10-123526421-A-C
• rs705170
• ENST00000662754.1:n.890+2017A>C

Variant summary

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

The ENST00000662754.1(LINC02641):​n.890+2017A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,104 control chromosomes in the GnomAD database, including 41,570 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 0.74 (41570 hom., cov: 32)
• Consequence: LINC02641 ENST00000662754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 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+2017A>C		intron	N/A
	LINC02641	ENST00000812699.1		n.274-26116A>C		intron	N/A
	LINC02641	ENST00000812701.1		n.294-26116A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112145 AN: 151986 Hom.: 41534 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.738 AC: 112237 AN: 152104 Hom.: 41570 Cov.: 32 AF XY: 0.742 AC XY: 55194 AN XY: 74358

African (AFR) AF: 0.691 AC: 28667 AN: 41472

American (AMR) AF: 0.782 AC: 11958 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3468

East Asian (EAS) AF: 0.862 AC: 4451 AN: 5164

South Asian (SAS) AF: 0.793 AC: 3821 AN: 4818

European-Finnish (FIN) AF: 0.773 AC: 8174 AN: 10572

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50087 AN: 68010

Other (OTH) AF: 0.745 AC: 1574 AN: 2114

Alfa AF: 0.735 Hom.: 23502

Bravo AF: 0.741

Asia WGS AF: 0.802 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs705170; hg19: chr10-125285937;