rs2486032

Positions:

• chr10-123530269-G-T

Variant summary

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

The ENST00000662754.1(LINC02641):​n.890+5865G>T 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 0.632 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

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=-0.88).
• 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/exons	MANE	UniProt
LINC02641	XR_007062326.1	n.9710+5865G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02641	ENST00000662754.1	n.890+5865G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.634

Alfa AF: 0.587 Hom.: 43717

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2486032; hg19: chr10-125289785;