rs9501062
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007109.3(TCF19):c.*1213T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 985,596 control chromosomes in the GnomAD database, including 994 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 0.064 ( 508 hom., cov: 32)
Exomes 𝑓: 0.027 ( 486 hom. )
Consequence
TCF19
NM_007109.3 3_prime_UTR
NM_007109.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.211
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF19 | NM_007109.3 | c.*1213T>C | 3_prime_UTR_variant | 4/4 | ENST00000376257.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF19 | ENST00000376257.8 | c.*1213T>C | 3_prime_UTR_variant | 4/4 | 1 | NM_007109.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0638 AC: 9696AN: 151916Hom.: 506 Cov.: 32
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GnomAD4 exome AF: 0.0271 AC: 22623AN: 833562Hom.: 486 Cov.: 32 AF XY: 0.0270 AC XY: 10384AN XY: 384958
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GnomAD4 genome ? AF: 0.0638 AC: 9700AN: 152034Hom.: 508 Cov.: 32 AF XY: 0.0651 AC XY: 4837AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at