chr10-124942738-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_017580.3(ZRANB1):c.245T>A(p.Met82Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,614,200 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017580.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZRANB1 | NM_017580.3 | c.245T>A | p.Met82Lys | missense_variant | 1/9 | ENST00000359653.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZRANB1 | ENST00000359653.4 | c.245T>A | p.Met82Lys | missense_variant | 1/9 | 1 | NM_017580.3 | P1 | |
ENST00000508096.1 | n.412T>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000315 AC: 48AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000310 AC: 78AN: 251348Hom.: 0 AF XY: 0.000294 AC XY: 40AN XY: 135834
GnomAD4 exome AF: 0.000326 AC: 477AN: 1461886Hom.: 2 Cov.: 31 AF XY: 0.000320 AC XY: 233AN XY: 727244
GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.245T>A (p.M82K) alteration is located in exon 1 (coding exon 1) of the ZRANB1 gene. This alteration results from a T to A substitution at nucleotide position 245, causing the methionine (M) at amino acid position 82 to be replaced by a lysine (K). 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