7-139026552-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080660.4(ZC3HAV1L):c.895G>A(p.Glu299Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,613,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080660.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZC3HAV1L | NM_080660.4 | c.895G>A | p.Glu299Lys | missense_variant | Exon 5 of 5 | ENST00000275766.2 | NP_542391.2 | |
ZC3HAV1L | XM_011516688.4 | c.886+156G>A | intron_variant | Intron 4 of 4 | XP_011514990.1 | |||
ZC3HAV1L | XM_006716176.4 | c.*298G>A | downstream_gene_variant | XP_006716239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250362Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135452
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461542Hom.: 0 Cov.: 30 AF XY: 0.0000385 AC XY: 28AN XY: 727116
GnomAD4 genome AF: 0.000112 AC: 17AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.895G>A (p.E299K) alteration is located in exon 5 (coding exon 5) of the ZC3HAV1L gene. This alteration results from a G to A substitution at nucleotide position 895, causing the glutamic acid (E) at amino acid position 299 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