chr22-29322332-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05
Variant links:

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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
show subpopulations
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
show subpopulations
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5763140; hg19: chr22-29718321; API