13-32311289-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001136571.2(ZAR1L):c.637C>T(p.Arg213Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00004 in 1,548,444 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001136571.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZAR1L | NM_001136571.2 | c.637C>T | p.Arg213Trp | missense_variant | 3/6 | ENST00000533490.7 | NP_001130043.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZAR1L | ENST00000533490.7 | c.637C>T | p.Arg213Trp | missense_variant | 3/6 | 5 | NM_001136571.2 | ENSP00000437289 | P1 | |
ZAR1L | ENST00000345108.6 | c.637C>T | p.Arg213Trp | missense_variant | 1/4 | 1 | ENSP00000344616 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000132 AC: 2AN: 151136Hom.: 0 AF XY: 0.0000249 AC XY: 2AN XY: 80266
GnomAD4 exome AF: 0.0000387 AC: 54AN: 1396162Hom.: 4 Cov.: 31 AF XY: 0.0000407 AC XY: 28AN XY: 688490
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2024 | The c.637C>T (p.R213W) alteration is located in exon 1 (coding exon 1) of the ZAR1L gene. This alteration results from a C to T substitution at nucleotide position 637, causing the arginine (R) at amino acid position 213 to be replaced by a tryptophan (W). 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