GeneBe

chr19-41854712-CCT-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.157 in 152,238 control chromosomes in the GnomAD database, including 2,139 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2139 hom., cov: 29)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.283

Publications

1 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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:
0.157
AC:
23919
AN:
152120
Hom.:
2140
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0655
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.147
Gnomad ASJ
AF:
0.208
Gnomad EAS
AF:
0.252
Gnomad SAS
AF:
0.174
Gnomad FIN
AF:
0.240
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.191
Gnomad OTH
AF:
0.172
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.157
AC:
23919
AN:
152238
Hom.:
2139
Cov.:
29
AF XY:
0.159
AC XY:
11865
AN XY:
74426
show subpopulations
African (AFR)
AF:
0.0654
AC:
2720
AN:
41572
American (AMR)
AF:
0.146
AC:
2238
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.208
AC:
722
AN:
3472
East Asian (EAS)
AF:
0.252
AC:
1307
AN:
5180
South Asian (SAS)
AF:
0.175
AC:
844
AN:
4830
European-Finnish (FIN)
AF:
0.240
AC:
2534
AN:
10578
Middle Eastern (MID)
AF:
0.214
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
0.191
AC:
12960
AN:
67996
Other (OTH)
AF:
0.170
AC:
359
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
1030
2060
3091
4121
5151
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
270
540
810
1080
1350
<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:
0.176
Hom.:
314
Bravo
AF:
0.147
Asia WGS
AF:
0.195
AC:
678
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.28

Splicing

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

Publications

Other links and lift over

dbSNP: rs3214574; hg19: chr19-42358780; API