3-12153526-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003256.4(TIMP4):c.664G>A(p.Val222Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003256.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TIMP4 | NM_003256.4 | c.664G>A | p.Val222Ile | missense_variant | 5/5 | ENST00000287814.5 | NP_003247.1 | |
SYN2 | NM_133625.6 | c.774+2200C>T | intron_variant | ENST00000621198.5 | NP_598328.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TIMP4 | ENST00000287814.5 | c.664G>A | p.Val222Ile | missense_variant | 5/5 | 1 | NM_003256.4 | ENSP00000287814 | P1 | |
SYN2 | ENST00000621198.5 | c.774+2200C>T | intron_variant | 1 | NM_133625.6 | ENSP00000480050 | P2 | |||
SYN2 | ENST00000620175.4 | c.774+2200C>T | intron_variant | 1 | ENSP00000484916 | A2 | ||||
SYN2 | ENST00000439861.5 | n.225+2200C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251432Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135886
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461164Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 726876
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at