rs2822686

Variant names:

• chr21-14479779-C-T
• rs2822686
• XR_007067925.1:n.339+2112C>T

Variant summary

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

The XR_007067925.1(LOC124905053):​n.339+2112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,006 control chromosomes in the GnomAD database, including 8,565 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 0.29 (8565 hom., cov: 31)
• Consequence: LOC124905053 XR_007067925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 2 publications found

Genes affected

LOC124905053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44070 AN: 151888 Hom.: 8534 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.290 AC: 44141 AN: 152006 Hom.: 8565 Cov.: 31 AF XY: 0.289 AC XY: 21472 AN XY: 74296

African (AFR) AF: 0.558 AC: 23086 AN: 41394

American (AMR) AF: 0.180 AC: 2744 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3470

East Asian (EAS) AF: 0.0548 AC: 284 AN: 5184

South Asian (SAS) AF: 0.262 AC: 1264 AN: 4816

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10566

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12868 AN: 67980

Other (OTH) AF: 0.261 AC: 553 AN: 2116

Alfa AF: 0.227 Hom.: 13041

Bravo AF: 0.295

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.64
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2822686; hg19: chr21-15852100;