7-100736877-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003386.3(ZAN):c.322G>A(p.Asp108Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000202 in 1,486,278 control chromosomes in the GnomAD database, including 6 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_003386.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZAN | NM_003386.3 | c.322G>A | p.Asp108Asn | missense_variant | 5/48 | ENST00000613979.5 | NP_003377.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZAN | ENST00000613979.5 | c.322G>A | p.Asp108Asn | missense_variant | 5/48 | 1 | NM_003386.3 | ENSP00000480750 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000494 AC: 7AN: 141692Hom.: 1 Cov.: 27
GnomAD3 exomes AF: 0.0000281 AC: 5AN: 177782Hom.: 0 AF XY: 0.0000310 AC XY: 3AN XY: 96642
GnomAD4 exome AF: 0.0000171 AC: 23AN: 1344586Hom.: 5 Cov.: 32 AF XY: 0.0000210 AC XY: 14AN XY: 666062
GnomAD4 genome AF: 0.0000494 AC: 7AN: 141692Hom.: 1 Cov.: 27 AF XY: 0.0000433 AC XY: 3AN XY: 69220
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at