chr22-29322332-C-T

Variant names:

• chr22-29322332-C-T
• rs5763140

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 0.106 in 152,240 control chromosomes in the GnomAD database, including 970 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 0.11 (970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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 (EAS) allele frequency at 95% confidence interval = 0.272 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: 0.106 AC: 16050 AN: 152122 Hom.: 970 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.106 AC: 16063 AN: 152240 Hom.: 970 Cov.: 32 AF XY: 0.104 AC XY: 7777 AN XY: 74428

Gnomad4 AFR AF: 0.0850

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.105

Alfa AF: 0.104 Hom.: 583

Bravo AF: 0.104

Asia WGS AF: 0.144 AC: 501 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	0.81
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5763140; hg19: chr22-29718321;