NM_007109.3:c.798-176T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007109.3(TCF19):​c.798-176T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 151,996 control chromosomes in the GnomAD database, including 46,548 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 0.78 ( 46548 hom., cov: 31)

Consequence

TCF19
NM_007109.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.842

Publications

31 publications found
Variant links:
Genes affected
TCF19 (HGNC:11629): (transcription factor 19) This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TCF19NM_007109.3 linkc.798-176T>C intron_variant Intron 3 of 3 ENST00000376257.8 NP_009040.2 Q9Y242A0A1U9X8M7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TCF19ENST00000376257.8 linkc.798-176T>C intron_variant Intron 3 of 3 1 NM_007109.3 ENSP00000365433.3 Q9Y242

Frequencies

GnomAD3 genomes
AF:
0.781
AC:
118558
AN:
151878
Hom.:
46509
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.847
Gnomad AMI
AF:
0.806
Gnomad AMR
AF:
0.805
Gnomad ASJ
AF:
0.862
Gnomad EAS
AF:
0.678
Gnomad SAS
AF:
0.688
Gnomad FIN
AF:
0.749
Gnomad MID
AF:
0.889
Gnomad NFE
AF:
0.748
Gnomad OTH
AF:
0.816
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.781
AC:
118651
AN:
151996
Hom.:
46548
Cov.:
31
AF XY:
0.780
AC XY:
57922
AN XY:
74302
show subpopulations
African (AFR)
AF:
0.847
AC:
35139
AN:
41462
American (AMR)
AF:
0.805
AC:
12297
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.862
AC:
2992
AN:
3470
East Asian (EAS)
AF:
0.679
AC:
3503
AN:
5160
South Asian (SAS)
AF:
0.687
AC:
3298
AN:
4798
European-Finnish (FIN)
AF:
0.749
AC:
7921
AN:
10578
Middle Eastern (MID)
AF:
0.884
AC:
260
AN:
294
European-Non Finnish (NFE)
AF:
0.748
AC:
50787
AN:
67934
Other (OTH)
AF:
0.815
AC:
1722
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1341
2682
4024
5365
6706
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
862
1724
2586
3448
4310
<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:
0.770
Hom.:
114680
Bravo
AF:
0.790
Asia WGS
AF:
0.755
AC:
2626
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
10
DANN
Benign
0.84
PhyloP100
-0.84
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: rs2073723; hg19: chr6-31130078; API