rs58667

chr22-45272131-C-T

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 0.478 in 152,050 control chromosomes in the GnomAD database, including 18,137 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 0.48 (18137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72654 AN: 151932 Hom.: 18110 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.478 AC: 72734 AN: 152050 Hom.: 18137 Cov.: 32 AF XY: 0.480 AC XY: 35646 AN XY: 74324

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.446

Alfa AF: 0.414 Hom.: 18370

Bravo AF: 0.494

Asia WGS AF: 0.486 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.44
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58667; hg19: chr22-45668012;