GeneBe

rs3810608

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 0.175 in 152,214 control chromosomes in the GnomAD database, including 2,719 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 ( 2719 hom., cov: 31)
Exomes 𝑓: 0.11 ( 0 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.05

Publications

9 publications found
Variant links:

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ACMG classification

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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:
0.175
AC:
26625
AN:
151904
Hom.:
2715
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0837
Gnomad AMI
AF:
0.228
Gnomad AMR
AF:
0.189
Gnomad ASJ
AF:
0.262
Gnomad EAS
AF:
0.0990
Gnomad SAS
AF:
0.0995
Gnomad FIN
AF:
0.171
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.234
Gnomad OTH
AF:
0.205
GnomAD4 exome
AF:
0.115
AC:
22
AN:
192
Hom.:
0
Cov.:
0
AF XY:
0.127
AC XY:
17
AN XY:
134
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
8
American (AMR)
AF:
0.00
AC:
0
AN:
2
Ashkenazi Jewish (ASJ)
AF:
0.250
AC:
1
AN:
4
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AF:
0.120
AC:
6
AN:
50
Middle Eastern (MID)
AF:
0.500
AC:
1
AN:
2
European-Non Finnish (NFE)
AF:
0.110
AC:
13
AN:
118
Other (OTH)
AF:
0.167
AC:
1
AN:
6
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.473
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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:
0.175
AC:
26630
AN:
152022
Hom.:
2719
Cov.:
31
AF XY:
0.172
AC XY:
12786
AN XY:
74304
show subpopulations
African (AFR)
AF:
0.0837
AC:
3471
AN:
41486
American (AMR)
AF:
0.189
AC:
2881
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.262
AC:
910
AN:
3468
East Asian (EAS)
AF:
0.0993
AC:
514
AN:
5178
South Asian (SAS)
AF:
0.0998
AC:
481
AN:
4818
European-Finnish (FIN)
AF:
0.171
AC:
1809
AN:
10564
Middle Eastern (MID)
AF:
0.238
AC:
70
AN:
294
European-Non Finnish (NFE)
AF:
0.233
AC:
15859
AN:
67922
Other (OTH)
AF:
0.203
AC:
428
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1096
2192
3289
4385
5481
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
284
568
852
1136
1420
<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:
0.191
Hom.:
471
Bravo
AF:
0.171
Asia WGS
AF:
0.102
AC:
356
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.17
DANN
Benign
0.60
PhyloP100
-3.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs3810608; hg19: chr22-22112794; COSMIC: COSV53189787; API