chr21-15520713-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000229425 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634644.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229425	ENST00000634644.1	TSL:5	n.355-6779C>T		intron	N/A
	ENSG00000229425	ENST00000634708.1	TSL:5	n.355-42857C>T		intron	N/A
	ENSG00000229425	ENST00000653886.1		n.331-6779C>T		intron	N/A

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

African (AFR) AF: 0.298 AC: 12338 AN: 41460

American (AMR) AF: 0.261 AC: 3992 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3470

East Asian (EAS) AF: 0.0783 AC: 406 AN: 5188

South Asian (SAS) AF: 0.202 AC: 971 AN: 4812

European-Finnish (FIN) AF: 0.203 AC: 2138 AN: 10548

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12792 AN: 67996

Other (OTH) AF: 0.253 AC: 534 AN: 2112

Alfa AF: 0.112 Hom.: 186

Bravo AF: 0.234

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2823322; hg19: chr21-16893032;