4-99374258-T-C

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 0.25 in 152,008 control chromosomes in the GnomAD database, including 5,552 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 0.25 ( 5552 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

1 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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 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:
0.250
AC:
37970
AN:
151890
Hom.:
5545
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.307
Gnomad AMI
AF:
0.254
Gnomad AMR
AF:
0.183
Gnomad ASJ
AF:
0.175
Gnomad EAS
AF:
0.675
Gnomad SAS
AF:
0.467
Gnomad FIN
AF:
0.172
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.199
Gnomad OTH
AF:
0.239
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.250
AC:
38004
AN:
152008
Hom.:
5552
Cov.:
32
AF XY:
0.257
AC XY:
19100
AN XY:
74320
show subpopulations
African (AFR)
AF:
0.307
AC:
12729
AN:
41432
American (AMR)
AF:
0.183
AC:
2798
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.175
AC:
608
AN:
3470
East Asian (EAS)
AF:
0.676
AC:
3487
AN:
5160
South Asian (SAS)
AF:
0.466
AC:
2242
AN:
4810
European-Finnish (FIN)
AF:
0.172
AC:
1817
AN:
10564
Middle Eastern (MID)
AF:
0.211
AC:
62
AN:
294
European-Non Finnish (NFE)
AF:
0.199
AC:
13528
AN:
67980
Other (OTH)
AF:
0.237
AC:
501
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1353
2705
4058
5410
6763
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
400
800
1200
1600
2000
<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:
0.212
Hom.:
1639
Bravo
AF:
0.250
Asia WGS
AF:
0.469
AC:
1628
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
3.3
DANN
Benign
0.63
PhyloP100
-1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs1121534; hg19: chr4-100295415; API