rs4821667

Variant names:

• chr22-37434045-C-A
• rs4821667

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 0.396 in 152,066 control chromosomes in the GnomAD database, including 17,653 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 0.40 (17653 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.395 AC: 60083 AN: 151948 Hom.: 17589 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.396 AC: 60199 AN: 152066 Hom.: 17653 Cov.: 32 AF XY: 0.397 AC XY: 29498 AN XY: 74330

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.355

Alfa AF: 0.234 Hom.: 7607

Bravo AF: 0.426

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4821667; hg19: chr22-37830081;