22-25409257-T-C

Variant names:

• chr22-25409257-T-C
• rs13057190

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 0.135 in 152,000 control chromosomes in the GnomAD database, including 1,729 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 0.14 (1729 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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: 0.135 AC: 20566 AN: 151882 Hom.: 1728 Cov.: 33

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.135 AC: 20562 AN: 152000 Hom.: 1729 Cov.: 33 AF XY: 0.134 AC XY: 9925 AN XY: 74294

Gnomad4 AFR AF: 0.0675

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.136

Alfa AF: 0.152 Hom.: 724

Bravo AF: 0.132

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13057190; hg19: chr22-25805224;