chr21-15520713-G-A

Variant names:

• chr21-15520713-G-A
• rs2823322
• ENST00000634644.1:n.355-6779C>T

Variant summary

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

The ENST00000634644.1(ENSG00000229425):​n.355-6779C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,080 control chromosomes in the GnomAD database, including 4,091 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 0.23 (4091 hom., cov: 32)
• Consequence: ENSG00000229425 ENST00000634644.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

ENSG00000229425 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) 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.355-6779C>T		intron_variant	Intron 2 of 11	5
ENSG00000229425	ENST00000634708.1	n.355-42857C>T		intron_variant	Intron 2 of 9	5
ENSG00000229425	ENST00000653886.1	n.331-6779C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34276 AN: 151962 Hom.: 4089 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.226 AC: 34294 AN: 152080 Hom.: 4091 Cov.: 32 AF XY: 0.226 AC XY: 16778 AN XY: 74332

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0783

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.253

Alfa AF: 0.102 Hom.: 143

Bravo AF: 0.234

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823322; hg19: chr21-16893032;