9-41133718-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001085457.2(ZNG1F):c.841G>A(p.Val281Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 151,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001085457.2 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 |
---|---|---|---|---|---|---|---|---|
ZNG1F | NM_001085457.2 | c.841G>A | p.Val281Ile | missense_variant | Exon 12 of 15 | ENST00000377391.8 | NP_001078926.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNG1F | ENST00000377391.8 | c.841G>A | p.Val281Ile | missense_variant | Exon 12 of 15 | 1 | NM_001085457.2 | ENSP00000366608.4 | ||
ZNG1F | ENST00000456520.5 | c.784G>A | p.Val262Ile | missense_variant | Exon 11 of 14 | 1 | ENSP00000401079.2 | |||
ZNG1F | ENST00000382436.7 | n.*386G>A | non_coding_transcript_exon_variant | Exon 13 of 16 | 1 | ENSP00000484049.1 | ||||
ZNG1F | ENST00000486387.6 | n.*1406G>A | non_coding_transcript_exon_variant | Exon 14 of 17 | 2 | ENSP00000480837.1 | ||||
ZNG1F | ENST00000382436.7 | n.*386G>A | 3_prime_UTR_variant | Exon 13 of 16 | 1 | ENSP00000484049.1 | ||||
ZNG1F | ENST00000486387.6 | n.*1406G>A | 3_prime_UTR_variant | Exon 14 of 17 | 2 | ENSP00000480837.1 |
Frequencies
GnomAD3 genomes AF: 0.000258 AC: 39AN: 150920Hom.: 0 Cov.: 28
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000665 AC: 96AN: 1444080Hom.: 0 Cov.: 41 AF XY: 0.0000807 AC XY: 58AN XY: 718800
GnomAD4 genome AF: 0.000258 AC: 39AN: 151042Hom.: 0 Cov.: 28 AF XY: 0.000203 AC XY: 15AN XY: 73790
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.841G>A (p.V281I) alteration is located in exon 12 (coding exon 12) of the CBWD6 gene. This alteration results from a G to A substitution at nucleotide position 841, causing the valine (V) at amino acid position 281 to be replaced by an isoleucine (I). 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