22-21625000-T-C

Variant names:

• chr22-21625000-T-C
• rs4821124

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 0.193 in 152,190 control chromosomes in the GnomAD database, including 3,528 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 0.19 (3528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

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 (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.193 AC: 29289 AN: 152072 Hom.: 3520 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.193 AC: 29308 AN: 152190 Hom.: 3528 Cov.: 32 AF XY: 0.204 AC XY: 15143 AN XY: 74394

Gnomad4 AFR AF: 0.0806

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.201

Alfa AF: 0.179 Hom.: 701

Bravo AF: 0.192

Asia WGS AF: 0.320 AC: 1114 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	0.14
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4821124; hg19: chr22-21979289;