3-196327574-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000273695.4(TM4SF19):c.17G>T(p.Cys6Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000273695.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TM4SF19 | NM_138461.4 | c.17G>T | p.Cys6Phe | missense_variant | 2/5 | ENST00000273695.4 | NP_612470.2 | |
TM4SF19 | NM_001204897.2 | c.17G>T | p.Cys6Phe | missense_variant | 2/5 | NP_001191826.1 | ||
TM4SF19 | NM_001204898.2 | c.17G>T | p.Cys6Phe | missense_variant | 2/4 | NP_001191827.1 | ||
TM4SF19-DYNLT2B | NR_037950.1 | n.175G>T | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TM4SF19 | ENST00000273695.4 | c.17G>T | p.Cys6Phe | missense_variant | 2/5 | 1 | NM_138461.4 | ENSP00000273695.4 | ||
TM4SF19 | ENST00000446879.5 | c.17G>T | p.Cys6Phe | missense_variant | 2/6 | 1 | ENSP00000395280.1 | |||
TM4SF19 | ENST00000454715.5 | c.17G>T | p.Cys6Phe | missense_variant | 2/4 | 1 | ENSP00000387728.1 | |||
TM4SF19-DYNLT2B | ENST00000442633.1 | n.17G>T | non_coding_transcript_exon_variant | 2/6 | 1 | ENSP00000405973.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152078Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 250872Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135696
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461282Hom.: 0 Cov.: 36 AF XY: 0.00000688 AC XY: 5AN XY: 726968
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152078Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.17G>T (p.C6F) alteration is located in exon 2 (coding exon 1) of the TM4SF19 gene. This alteration results from a G to T substitution at nucleotide position 17, causing the cysteine (C) at amino acid position 6 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at