rs2836823

Variant names:

• chr21-39008323-C-T
• rs2836823
• ENST00000419664.1:n.243-92G>A

Variant summary

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

The ENST00000652155.1(LINC02940):​n.1432-1539G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 21 publications found

Genes affected

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

ENSG00000296867 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652155.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02940	ENST00000419664.1	TSL:5	n.243-92G>A		intron	N/A
	LINC02940	ENST00000652155.1		n.1432-1539G>A		intron	N/A
	ENSG00000296867	ENST00000743249.1		n.114-517C>T		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.591 AC: 13 AN: 22

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0842 AC: 3499 AN: 41534

American (AMR) AF: 0.352 AC: 5379 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3468

East Asian (EAS) AF: 0.0436 AC: 226 AN: 5180

South Asian (SAS) AF: 0.195 AC: 940 AN: 4828

European-Finnish (FIN) AF: 0.404 AC: 4266 AN: 10562

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30535 AN: 67984

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.399 Hom.: 55048

Bravo AF: 0.299

Asia WGS AF: 0.125 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.20
PhyloP100		-0.73

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2836823;

hg19: chr21-40380249;