chr7-72807317-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001145440.3(TYW1B):c.472G>A(p.Val158Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000335 in 1,614,014 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145440.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TYW1B | NM_001145440.3 | c.472G>A | p.Val158Met | missense_variant | Exon 5 of 14 | ENST00000620995.5 | NP_001138912.2 | |
TYW1B | NM_001412179.1 | c.472G>A | p.Val158Met | missense_variant | Exon 5 of 12 | NP_001399108.1 | ||
TYW1B | NM_001412180.1 | c.472G>A | p.Val158Met | missense_variant | Exon 5 of 11 | NP_001399109.1 | ||
TYW1B | NM_001412181.1 | c.472G>A | p.Val158Met | missense_variant | Exon 5 of 5 | NP_001399110.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TYW1B | ENST00000620995.5 | c.472G>A | p.Val158Met | missense_variant | Exon 5 of 14 | 1 | NM_001145440.3 | ENSP00000482502.1 | ||
TYW1B | ENST00000612372.4 | c.238-4795G>A | intron_variant | Intron 3 of 11 | 1 | ENSP00000480534.1 | ||||
TYW1B | ENST00000610600.1 | c.277G>A | p.Val93Met | missense_variant | Exon 4 of 8 | 2 | ENSP00000484480.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251292Hom.: 1 AF XY: 0.0000589 AC XY: 8AN XY: 135810
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461740Hom.: 2 Cov.: 87 AF XY: 0.0000399 AC XY: 29AN XY: 727148
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.472G>A (p.V158M) alteration is located in exon 5 (coding exon 5) of the TYW1B gene. This alteration results from a G to A substitution at nucleotide position 472, causing the valine (V) at amino acid position 158 to be replaced by a methionine (M). 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