rs2823286

Variant names:

• chr21-15445619-G-A
• rs2823286
• ENST00000634644.1:n.952+21669C>T

Variant summary

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

The ENST00000634644.1(ENSG00000229425):​n.952+21669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,102 control chromosomes in the GnomAD database, including 5,758 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 0.27 (5758 hom., cov: 30)
• Consequence: ENSG00000229425 ENST00000634644.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

Genes affected

ENSG00000229425 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229425	ENST00000634644.1	n.952+21669C>T		intron_variant	Intron 8 of 11	5
ENSG00000229425	ENST00000634708.1	n.423+32169C>T		intron_variant	Intron 3 of 9	5
ENSG00000229425	ENST00000654045.1	n.734-1538C>T		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41385 AN: 150984 Hom.: 5754 Cov.: 30

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.274 AC: 41409 AN: 151102 Hom.: 5758 Cov.: 30 AF XY: 0.267 AC XY: 19723 AN XY: 73766

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.275

Alfa AF: 0.289 Hom.: 12972

Bravo AF: 0.282

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.50
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823286; hg19: chr21-16817938;