GeneBe

rs4821494

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 0.583 in 148,838 control chromosomes in the GnomAD database, including 27,173 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 0.58 ( 27166 hom., cov: 22)
Exomes 𝑓: 0.52 ( 7 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.347

Publications

12 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=-0.78).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 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:
0.583
AC:
86692
AN:
148684
Hom.:
27159
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.388
Gnomad AMI
AF:
0.773
Gnomad AMR
AF:
0.678
Gnomad ASJ
AF:
0.589
Gnomad EAS
AF:
0.255
Gnomad SAS
AF:
0.343
Gnomad FIN
AF:
0.615
Gnomad MID
AF:
0.558
Gnomad NFE
AF:
0.712
Gnomad OTH
AF:
0.619
GnomAD4 exome
AF:
0.522
AC:
24
AN:
46
Hom.:
7
AF XY:
0.474
AC XY:
18
AN XY:
38
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.412
AC:
14
AN:
34
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.833
AC:
10
AN:
12
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.583
AC:
86724
AN:
148792
Hom.:
27166
Cov.:
22
AF XY:
0.575
AC XY:
41660
AN XY:
72470
show subpopulations
African (AFR)
AF:
0.388
AC:
15648
AN:
40348
American (AMR)
AF:
0.679
AC:
10073
AN:
14842
Ashkenazi Jewish (ASJ)
AF:
0.589
AC:
2028
AN:
3446
East Asian (EAS)
AF:
0.254
AC:
1280
AN:
5038
South Asian (SAS)
AF:
0.344
AC:
1609
AN:
4682
European-Finnish (FIN)
AF:
0.615
AC:
6252
AN:
10164
Middle Eastern (MID)
AF:
0.559
AC:
161
AN:
288
European-Non Finnish (NFE)
AF:
0.712
AC:
47728
AN:
67050
Other (OTH)
AF:
0.615
AC:
1257
AN:
2044
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
1487
2973
4460
5946
7433
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
704
1408
2112
2816
3520
<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:
0.615
Hom.:
4486
Bravo
AF:
0.585
Asia WGS
AF:
0.327
AC:
1138
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
2.4
DANN
Benign
0.65
PhyloP100
-0.35
PromoterAI
0.031
Neutral
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs4821494; hg19: chr22-36878160; API