rs2057227

chr10-33912923-G-Achr10-33912923-G-C

Variant summary

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

The NR_170279.1(LINC02629):n.712+90G>A 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 0.654 in 151,678 control chromosomes in the GnomAD database, including 32,735 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 0.65 (32721 hom., cov: 30)
  • Exomes 𝑓: 0.49 (14 hom.)
• Consequence: LINC02629 NR_170279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

LINC02629 (HGNC:54108): (long intergenic non-protein coding RNA 2629)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02629	NR_170279.1	n.712+90G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02629	ENST00000434552.3	n.370+90G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99018 AN: 151452 Hom.: 32704 Cov.: 30

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.659

GnomAD4 exome AF: 0.491 AC: 53 AN: 108 Hom.: 14 AF XY: 0.530 AC XY: 35 AN XY: 66

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.424

Gnomad4 NFE exome AF: 0.567

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.654 AC: 99083 AN: 151570 Hom.: 32721 Cov.: 30 AF XY: 0.663 AC XY: 49116 AN XY: 74080

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.657

Alfa AF: 0.625 Hom.: 37844

Bravo AF: 0.657

Asia WGS AF: 0.714 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.021
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057227; hg19: chr10-34201851;