9-41183657-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001085457.2(ZNG1F):c.245G>T(p.Ser82Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000305 in 1,605,298 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a pathogenic 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNG1F | NM_001085457.2 | c.245G>T | p.Ser82Ile | missense_variant | Exon 3 of 15 | ENST00000377391.8 | NP_001078926.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNG1F | ENST00000377391.8 | c.245G>T | p.Ser82Ile | missense_variant | Exon 3 of 15 | 1 | NM_001085457.2 | ENSP00000366608.4 | ||
ZNG1F | ENST00000456520.5 | c.245G>T | p.Ser82Ile | missense_variant | Exon 3 of 14 | 1 | ENSP00000401079.2 | |||
ZNG1F | ENST00000382436.7 | n.113G>T | non_coding_transcript_exon_variant | Exon 3 of 16 | 1 | ENSP00000484049.1 | ||||
ZNG1F | ENST00000486387.6 | n.245G>T | non_coding_transcript_exon_variant | Exon 3 of 17 | 2 | ENSP00000480837.1 |
Frequencies
GnomAD3 genomes AF: 0.000148 AC: 22AN: 149138Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249784Hom.: 1 AF XY: 0.0000592 AC XY: 8AN XY: 135104
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1456160Hom.: 4 Cov.: 34 AF XY: 0.0000179 AC XY: 13AN XY: 724450
GnomAD4 genome AF: 0.000148 AC: 22AN: 149138Hom.: 0 Cov.: 27 AF XY: 0.000138 AC XY: 10AN XY: 72714
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.245G>T (p.S82I) alteration is located in exon 3 (coding exon 3) of the CBWD6 gene. This alteration results from a G to T substitution at nucleotide position 245, causing the serine (S) at amino acid position 82 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