chr4-103589846-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001059.3(TACR3):c.1234G>A(p.Val412Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001059.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TACR3 | NM_001059.3 | c.1234G>A | p.Val412Met | missense_variant | 5/5 | ENST00000304883.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TACR3 | ENST00000304883.3 | c.1234G>A | p.Val412Met | missense_variant | 5/5 | 1 | NM_001059.3 | P1 | |
TACR3-AS1 | ENST00000502936.1 | n.190-1361C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
TACR3-AS1 | ENST00000512401.5 | n.292-1361C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251080Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135666
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461680Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727134
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Submissions by phenotype
Hypogonadotropic hypogonadism 11 with or without anosmia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 11, 2021 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at