22-20379205-T-G

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 0.182 in 152,164 control chromosomes in the GnomAD database, including 4,181 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 0.18 ( 4181 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0840
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 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:
0.182
AC:
27668
AN:
152046
Hom.:
4178
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.418
Gnomad AMI
AF:
0.166
Gnomad AMR
AF:
0.119
Gnomad ASJ
AF:
0.118
Gnomad EAS
AF:
0.00596
Gnomad SAS
AF:
0.0609
Gnomad FIN
AF:
0.0867
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0940
Gnomad OTH
AF:
0.157
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.182
AC:
27692
AN:
152164
Hom.:
4181
Cov.:
32
AF XY:
0.177
AC XY:
13138
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.418
Gnomad4 AMR
AF:
0.119
Gnomad4 ASJ
AF:
0.118
Gnomad4 EAS
AF:
0.00578
Gnomad4 SAS
AF:
0.0603
Gnomad4 FIN
AF:
0.0867
Gnomad4 NFE
AF:
0.0940
Gnomad4 OTH
AF:
0.156
Alfa
AF:
0.100
Hom.:
1072
Bravo
AF:
0.193
Asia WGS
AF:
0.0610
AC:
215
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.6
DANN
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs6003971; hg19: chr22-20733495; API