rs2486032

Variant names:

• chr10-123530269-G-T
• rs2486032
• ENST00000662754.1:n.890+5865G>T

Variant summary

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

The ENST00000662754.1(LINC02641):​n.890+5865G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 146,138 control chromosomes in the GnomAD database, including 29,711 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 0.63 (29711 hom., cov: 22)
• Consequence: LINC02641 ENST00000662754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747616.2	n.1639+5865G>T		intron_variant	Intron 3 of 5
LINC02641	XR_001747617.3	n.918+5865G>T		intron_variant	Intron 4 of 6
LINC02641	XR_001747618.2	n.896+5865G>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000662754.1	n.890+5865G>T		intron_variant	Intron 3 of 3
LINC02641	ENST00000812699.1	n.274-22268G>T		intron_variant	Intron 2 of 3
LINC02641	ENST00000812701.1	n.294-22268G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.632 AC: 92293 AN: 146054 Hom.: 29675 Cov.: 22

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.632 AC: 92372 AN: 146138 Hom.: 29711 Cov.: 22 AF XY: 0.630 AC XY: 44463 AN XY: 70596

African (AFR) AF: 0.777 AC: 30935 AN: 39816

American (AMR) AF: 0.604 AC: 8761 AN: 14508

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2175 AN: 3452

East Asian (EAS) AF: 0.393 AC: 1903 AN: 4846

South Asian (SAS) AF: 0.417 AC: 1887 AN: 4528

European-Finnish (FIN) AF: 0.616 AC: 5495 AN: 8914

Middle Eastern (MID) AF: 0.629 AC: 171 AN: 272

European-Non Finnish (NFE) AF: 0.586 AC: 39185 AN: 66900

Other (OTH) AF: 0.634 AC: 1271 AN: 2004

Alfa AF: 0.598 Hom.: 74454

Bravo AF: 0.632

Asia WGS AF: 0.437 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.43
DANN	Benign	0.85
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2486032; hg19: chr10-125289785;