chr1-74738690-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138467.3(TYW3):c.256A>G(p.Ile86Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000443 in 1,601,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138467.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYW3 | NM_138467.3 | c.256A>G | p.Ile86Val | missense_variant, splice_region_variant | 3/6 | ENST00000370867.8 | |
TYW3 | XM_006710347.3 | c.256A>G | p.Ile86Val | missense_variant, splice_region_variant | 3/7 | ||
TYW3 | NM_001162916.2 | c.255+2068A>G | intron_variant | ||||
TYW3 | NR_027962.2 | n.462A>G | splice_region_variant, non_coding_transcript_exon_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYW3 | ENST00000370867.8 | c.256A>G | p.Ile86Val | missense_variant, splice_region_variant | 3/6 | 1 | NM_138467.3 | P1 | |
TYW3 | ENST00000479111.5 | c.-105A>G | splice_region_variant, 5_prime_UTR_variant | 4/7 | 3 | ||||
TYW3 | ENST00000483990.1 | c.-105A>G | splice_region_variant, 5_prime_UTR_variant | 2/4 | 3 | ||||
TYW3 | ENST00000457880.6 | c.255+2068A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250354Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135318
GnomAD4 exome AF: 0.0000462 AC: 67AN: 1449596Hom.: 0 Cov.: 30 AF XY: 0.0000500 AC XY: 36AN XY: 720652
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2021 | The c.256A>G (p.I86V) alteration is located in exon 3 (coding exon 3) of the TYW3 gene. This alteration results from a A to G substitution at nucleotide position 256, causing the isoleucine (I) at amino acid position 86 to be replaced by a valine (V). 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