3-12158719-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003256.4(TIMP4):āc.122T>Cā(p.Ile41Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000214 in 1,610,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003256.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TIMP4 | NM_003256.4 | c.122T>C | p.Ile41Thr | missense_variant | 1/5 | ENST00000287814.5 | |
SYN2 | NM_133625.6 | c.775-2827A>G | intron_variant | ENST00000621198.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIMP4 | ENST00000287814.5 | c.122T>C | p.Ile41Thr | missense_variant | 1/5 | 1 | NM_003256.4 | P1 | |
SYN2 | ENST00000621198.5 | c.775-2827A>G | intron_variant | 1 | NM_133625.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000826 AC: 20AN: 242114Hom.: 0 AF XY: 0.0000679 AC XY: 9AN XY: 132504
GnomAD4 exome AF: 0.000223 AC: 325AN: 1457952Hom.: 0 Cov.: 31 AF XY: 0.000192 AC XY: 139AN XY: 725514
GnomAD4 genome AF: 0.000125 AC: 19AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2023 | The c.122T>C (p.I41T) alteration is located in exon 1 (coding exon 1) of the TIMP4 gene. This alteration results from a T to C substitution at nucleotide position 122, causing the isoleucine (I) at amino acid position 41 to be replaced by a threonine (T). 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