NM_017757.3:c.4146G>A
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_017757.3(ZNF407):c.4146G>A(p.Thr1382Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,613,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017757.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomaliesInheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- intellectual disabilityInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- complex neurodevelopmental disorderInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.4146G>A | p.Thr1382Thr | synonymous_variant | Exon 2 of 9 | 1 | NM_017757.3 | ENSP00000299687.4 | ||
ZNF407 | ENST00000577538.5 | c.4146G>A | p.Thr1382Thr | synonymous_variant | Exon 1 of 7 | 2 | ENSP00000463270.1 | |||
ZNF407 | ENST00000309902.10 | c.4146G>A | p.Thr1382Thr | synonymous_variant | Exon 1 of 4 | 2 | ENSP00000310359.5 | |||
ZNF407 | ENST00000582337.5 | c.4146G>A | p.Thr1382Thr | synonymous_variant | Exon 2 of 5 | 5 | ENSP00000462348.1 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152158Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000369 AC: 92AN: 249204 AF XY: 0.000288 show subpopulations
GnomAD4 exome AF: 0.000209 AC: 306AN: 1461706Hom.: 0 Cov.: 41 AF XY: 0.000208 AC XY: 151AN XY: 727136 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000355 AC: 54AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.000296 AC XY: 22AN XY: 74322 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
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ZNF407-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at