rs2836823

chr21-39008323-C-T

Variant summary

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

The ENST00000652155.1(LINC02940):n.1432-1539G>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 0.309 in 152,180 control chromosomes in the GnomAD database, including 9,337 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 0.31 (9334 hom., cov: 32)
  • Exomes 𝑓: 0.46 (3 hom.)
• Consequence: LINC02940 ENST00000652155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

Genes affected

LINC02940 (HGNC:55955): (long intergenic non-protein coding RNA 2940)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02940	XR_007067867.1	n.6954-1539G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02940	ENST00000652155.1	n.1432-1539G>A		intron_variant, non_coding_transcript_variant
LINC02940	ENST00000419664.1	n.243-92G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46976 AN: 152034 Hom.: 9337 Cov.: 32

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.293

GnomAD4 exome AF: 0.464 AC: 13 AN: 28 Hom.: 3 AF XY: 0.400 AC XY: 8 AN XY: 20

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.591

GnomAD4 genome AF: 0.309 AC: 46982 AN: 152152 Hom.: 9334 Cov.: 32 AF XY: 0.304 AC XY: 22618 AN XY: 74358

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.0436

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.294

Alfa AF: 0.417 Hom.: 26215

Bravo AF: 0.299

Asia WGS AF: 0.125 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.70
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836823; hg19: chr21-40380249;