chr7-76425002-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001110354.2(ZP3):āc.38T>Cā(p.Leu13Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000831 in 1,563,906 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001110354.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000115 AC: 2AN: 173774Hom.: 0 AF XY: 0.0000107 AC XY: 1AN XY: 93866
GnomAD4 exome AF: 0.00000496 AC: 7AN: 1411756Hom.: 0 Cov.: 30 AF XY: 0.00000716 AC XY: 5AN XY: 698292
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.38T>C (p.L13P) alteration is located in exon 1 (coding exon 1) of the ZP3 gene. This alteration results from a T to C substitution at nucleotide position 38, causing the leucine (L) at amino acid position 13 to be replaced by a proline (P). 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