21-43342571-C-G

Variant names:

• chr21-43342571-C-G
• rs12483177

Variant summary

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

The variant allele was found at a frequency of 0.221 in 152,024 control chromosomes in the GnomAD database, including 3,802 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 0.22 (3802 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33518 AN: 151906 Hom.: 3798 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.221 AC: 33551 AN: 152024 Hom.: 3802 Cov.: 33 AF XY: 0.216 AC XY: 16032 AN XY: 74300

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.215

Alfa AF: 0.113 Hom.: 192

Bravo AF: 0.221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.63
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12483177; hg19: chr21-44762451;