NM_021943.3:c.257C>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021943.3(ZFAND3):c.257C>T(p.Pro86Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021943.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFAND3 | NM_021943.3 | c.257C>T | p.Pro86Leu | missense_variant | Exon 3 of 6 | ENST00000287218.9 | NP_068762.1 | |
ZFAND3 | NM_001410904.1 | c.257C>T | p.Pro86Leu | missense_variant | Exon 3 of 5 | NP_001397833.1 | ||
ZFAND3 | XM_017011171.3 | c.209C>T | p.Pro70Leu | missense_variant | Exon 2 of 5 | XP_016866660.1 | ||
ZFAND3 | XM_011514790.3 | c.257C>T | p.Pro86Leu | missense_variant | Exon 3 of 5 | XP_011513092.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251246Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135784
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461846Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727224
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.257C>T (p.P86L) alteration is located in exon 3 (coding exon 3) of the ZFAND3 gene. This alteration results from a C to T substitution at nucleotide position 257, causing the proline (P) at amino acid position 86 to be replaced by a leucine (L). 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