3-60112188-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002012.4(FHIT):c.104-98036G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 151,984 control chromosomes in the GnomAD database, including 39,648 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 0.72 ( 39648 hom., cov: 31)
Consequence
FHIT
NM_002012.4 intron
NM_002012.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.658
Publications
2 publications found
Genes affected
FHIT (HGNC:3701): (fragile histidine triad diadenosine triphosphatase) The protein encoded by this gene is a P1-P3-bis(5'-adenosyl) triphosphate hydrolase involved in purine metabolism. This gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas. The encoded protein is also a tumor suppressor, as loss of its activity results in replication stress and DNA damage. [provided by RefSeq, Aug 2017]
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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=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FHIT | NM_002012.4 | c.104-98036G>A | intron_variant | Intron 5 of 9 | ENST00000492590.6 | NP_002003.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.720 AC: 109321AN: 151866Hom.: 39616 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
109321
AN:
151866
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.720 AC: 109410AN: 151984Hom.: 39648 Cov.: 31 AF XY: 0.720 AC XY: 53490AN XY: 74258 show subpopulations
GnomAD4 genome
AF:
AC:
109410
AN:
151984
Hom.:
Cov.:
31
AF XY:
AC XY:
53490
AN XY:
74258
show subpopulations
African (AFR)
AF:
AC:
33076
AN:
41468
American (AMR)
AF:
AC:
11003
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
2215
AN:
3448
East Asian (EAS)
AF:
AC:
4073
AN:
5146
South Asian (SAS)
AF:
AC:
3893
AN:
4802
European-Finnish (FIN)
AF:
AC:
6979
AN:
10560
Middle Eastern (MID)
AF:
AC:
175
AN:
294
European-Non Finnish (NFE)
AF:
AC:
46014
AN:
67980
Other (OTH)
AF:
AC:
1438
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1585
3169
4754
6338
7923
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
842
1684
2526
3368
4210
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2731
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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