22-37008126-A-C

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 0.165 in 152,250 control chromosomes in the GnomAD database, including 2,682 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 0.17 ( 2682 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.787
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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:
0.165
AC:
25106
AN:
152132
Hom.:
2679
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.305
Gnomad AMI
AF:
0.112
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.0965
Gnomad EAS
AF:
0.00500
Gnomad SAS
AF:
0.0855
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.110
Gnomad OTH
AF:
0.147
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.165
AC:
25151
AN:
152250
Hom.:
2682
Cov.:
33
AF XY:
0.162
AC XY:
12078
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.305
Gnomad4 AMR
AF:
0.166
Gnomad4 ASJ
AF:
0.0965
Gnomad4 EAS
AF:
0.00501
Gnomad4 SAS
AF:
0.0860
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.110
Gnomad4 OTH
AF:
0.144
Alfa
AF:
0.133
Hom.:
937
Bravo
AF:
0.177
Asia WGS
AF:
0.0630
AC:
220
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.75
DANN
Benign
0.85

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: rs16997638; hg19: chr22-37404167; API