rs845086

Positions:

• chr10-123454284-A-C
• chr10-123454284-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662754.1(LINC02641):​n.338-69568A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,028 control chromosomes in the GnomAD database, including 20,057 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 0.49 (20057 hom., cov: 32)
• Consequence: LINC02641 ENST00000662754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

LINC02641 (HGNC:54125): (long intergenic non-protein coding RNA 2641)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02641	XR_007062326.1	n.9069+4772A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02641	ENST00000662754.1	n.338-69568A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74978 AN: 151910 Hom.: 20046 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.493 AC: 75006 AN: 152028 Hom.: 20057 Cov.: 32 AF XY: 0.494 AC XY: 36696 AN XY: 74308

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.522

Alfa AF: 0.553 Hom.: 4737

Bravo AF: 0.481

Asia WGS AF: 0.529 AC: 1841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845086; hg19: chr10-125213800;