chr6-136191773-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018945.4(PDE7B):c.1286G>A(p.Ser429Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000698 in 1,432,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018945.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE7B | NM_018945.4 | c.1286G>A | p.Ser429Asn | missense_variant | 13/13 | ENST00000308191.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE7B | ENST00000308191.11 | c.1286G>A | p.Ser429Asn | missense_variant | 13/13 | 1 | NM_018945.4 | P1 | |
PDE7B-AS1 | ENST00000655618.1 | n.82-29425C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000154 AC: 3AN: 195298Hom.: 0 AF XY: 0.0000189 AC XY: 2AN XY: 105636
GnomAD4 exome AF: 0.00000698 AC: 10AN: 1432992Hom.: 0 Cov.: 31 AF XY: 0.00000704 AC XY: 5AN XY: 710704
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.1286G>A (p.S429N) alteration is located in exon 13 (coding exon 13) of the PDE7B gene. This alteration results from a G to A substitution at nucleotide position 1286, causing the serine (S) at amino acid position 429 to be replaced by an asparagine (N). 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