X-135349117-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_152695.6(ZNF449):āc.362T>Cā(p.Met121Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000909 in 1,210,031 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152695.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF449 | NM_152695.6 | c.362T>C | p.Met121Thr | missense_variant | 3/5 | ENST00000339249.5 | |
ZNF449 | XM_047441914.1 | c.362T>C | p.Met121Thr | missense_variant | 3/5 | ||
ZNF449 | XM_017029351.2 | c.17T>C | p.Met6Thr | missense_variant | 4/6 | ||
ZNF449 | XM_047441915.1 | c.17T>C | p.Met6Thr | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF449 | ENST00000339249.5 | c.362T>C | p.Met121Thr | missense_variant | 3/5 | 1 | NM_152695.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 111925Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34075
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183274Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67716
GnomAD4 exome AF: 0.00000637 AC: 7AN: 1098106Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 4AN XY: 363462
GnomAD4 genome AF: 0.0000357 AC: 4AN: 111925Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34075
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.362T>C (p.M121T) alteration is located in exon 3 (coding exon 2) of the ZNF449 gene. This alteration results from a T to C substitution at nucleotide position 362, causing the methionine (M) at amino acid position 121 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