7-100057771-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_145914.3(ZSCAN21):c.473C>T(p.Pro158Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_145914.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZSCAN21 | ENST00000292450.9 | c.473C>T | p.Pro158Leu | missense_variant | Exon 3 of 4 | 1 | NM_145914.3 | ENSP00000292450.4 | ||
ZSCAN21 | ENST00000456748.6 | c.473C>T | p.Pro158Leu | missense_variant | Exon 3 of 5 | 5 | ENSP00000390960.2 | |||
ZSCAN21 | ENST00000438937.1 | c.473C>T | p.Pro158Leu | missense_variant | Exon 4 of 4 | 2 | ENSP00000404207.1 | |||
ZSCAN21 | ENST00000477297.1 | n.569C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152084Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251324 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727206 show subpopulations
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74290 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
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