chr17-78870935-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BA1
The NM_003255.5(TIMP2):c.303G>A(p.Ser101Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,611,508 control chromosomes in the GnomAD database, including 13,842 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_003255.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TIMP2 | NM_003255.5 | c.303G>A | p.Ser101Ser | synonymous_variant | Exon 3 of 5 | ENST00000262768.11 | NP_003246.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.117 AC: 17850AN: 152102Hom.: 1208 Cov.: 32
GnomAD3 exomes AF: 0.133 AC: 33339AN: 249848Hom.: 2663 AF XY: 0.138 AC XY: 18651AN XY: 134966
GnomAD4 exome AF: 0.126 AC: 184176AN: 1459288Hom.: 12637 Cov.: 31 AF XY: 0.129 AC XY: 93521AN XY: 725800
GnomAD4 genome AF: 0.117 AC: 17851AN: 152220Hom.: 1205 Cov.: 32 AF XY: 0.118 AC XY: 8794AN XY: 74418
ClinVar
Submissions by phenotype
TIMP2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at