rs13057533

Variant names:

• chr22-30214742-C-T
• rs13057533

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 0.192 in 152,138 control chromosomes in the GnomAD database, including 3,607 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 (3607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

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 (NFE) allele frequency at 95% confidence interval = 0.279 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: 0.192 AC: 29231 AN: 152020 Hom.: 3612 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.192 AC: 29220 AN: 152138 Hom.: 3607 Cov.: 32 AF XY: 0.188 AC XY: 14004 AN XY: 74374

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.214

Alfa AF: 0.237 Hom.: 1394

Bravo AF: 0.186

Asia WGS AF: 0.0810 AC: 286 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	1.8
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: rs13057533; hg19: chr22-30610731;