rs2823286

chr21-15445619-G-A

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, non coding transcript 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: ENST00000634644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634644.1	n.952+21669C>T		intron_variant, non_coding_transcript_variant		5

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;