GeneBe

chr22-36537621-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.376 in 732,054 control chromosomes in the GnomAD database, including 52,632 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 0.39 ( 11927 hom., cov: 31)
Exomes 𝑓: 0.37 ( 40705 hom. )

Consequence

LOC100500719
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980

Publications

1 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC100500719 n.36537621G>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000188078ENST00000339367.4 linkn.-17C>T upstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.393
AC:
59659
AN:
151948
Hom.:
11902
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.449
Gnomad AMI
AF:
0.444
Gnomad AMR
AF:
0.383
Gnomad ASJ
AF:
0.400
Gnomad EAS
AF:
0.227
Gnomad SAS
AF:
0.372
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.440
Gnomad NFE
AF:
0.376
Gnomad OTH
AF:
0.368
GnomAD4 exome
AF:
0.372
AC:
215568
AN:
579988
Hom.:
40705
Cov.:
3
AF XY:
0.372
AC XY:
117626
AN XY:
315824
show subpopulations
African (AFR)
AF:
0.451
AC:
7495
AN:
16628
American (AMR)
AF:
0.365
AC:
13760
AN:
37694
Ashkenazi Jewish (ASJ)
AF:
0.402
AC:
7935
AN:
19760
East Asian (EAS)
AF:
0.226
AC:
7699
AN:
34094
South Asian (SAS)
AF:
0.391
AC:
25782
AN:
65886
European-Finnish (FIN)
AF:
0.373
AC:
15721
AN:
42106
Middle Eastern (MID)
AF:
0.440
AC:
1714
AN:
3892
European-Non Finnish (NFE)
AF:
0.376
AC:
123729
AN:
328746
Other (OTH)
AF:
0.376
AC:
11733
AN:
31182
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
7193
14386
21579
28772
35965
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
742
1484
2226
2968
3710
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.393
AC:
59723
AN:
152066
Hom.:
11927
Cov.:
31
AF XY:
0.390
AC XY:
28999
AN XY:
74326
show subpopulations
African (AFR)
AF:
0.449
AC:
18643
AN:
41476
American (AMR)
AF:
0.383
AC:
5845
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.400
AC:
1387
AN:
3470
East Asian (EAS)
AF:
0.227
AC:
1171
AN:
5156
South Asian (SAS)
AF:
0.373
AC:
1795
AN:
4812
European-Finnish (FIN)
AF:
0.382
AC:
4047
AN:
10584
Middle Eastern (MID)
AF:
0.446
AC:
131
AN:
294
European-Non Finnish (NFE)
AF:
0.376
AC:
25532
AN:
67980
Other (OTH)
AF:
0.364
AC:
768
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1830
3660
5490
7320
9150
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
584
1168
1752
2336
2920
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.387
Hom.:
2309
Bravo
AF:
0.394
Asia WGS
AF:
0.300
AC:
1041
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
0.18
DANN
Benign
0.57
PhyloP100
-0.098

Splicing

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

Publications

Other links and lift over

dbSNP: rs2142824; hg19: chr22-36933668; COSMIC: COSV59546486; API