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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747616.2	n.1639+2017A>C		intron_variant	Intron 3 of 5
LINC02641	XR_001747617.3	n.918+2017A>C		intron_variant	Intron 4 of 6
LINC02641	XR_001747618.2	n.896+2017A>C		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000662754.1	n.890+2017A>C		intron_variant	Intron 3 of 3
LINC02641	ENST00000812699.1	n.274-26116A>C		intron_variant	Intron 2 of 3
LINC02641	ENST00000812701.1	n.294-26116A>C		intron_variant	Intron 2 of 3

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 v4.3

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;