chr17-46872574-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003396.3(WNT9B):c.135G>A(p.Pro45=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000614 in 1,600,106 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P45P) has been classified as Likely benign.
Frequency
Consequence
NM_003396.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.135G>A | p.Pro45= | synonymous_variant | 2/4 | ENST00000290015.7 | |
WNT9B | NM_001320458.2 | c.135G>A | p.Pro45= | synonymous_variant | 2/5 | ||
WNT9B | XM_011525178.3 | c.153G>A | p.Pro51= | synonymous_variant | 2/4 | ||
LRRC37A2 | XM_024450773.2 | c.4810-176482G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.135G>A | p.Pro45= | synonymous_variant | 2/4 | 1 | NM_003396.3 | P1 | |
WNT9B | ENST00000393461.2 | c.135G>A | p.Pro45= | synonymous_variant | 2/5 | 2 | |||
WNT9B | ENST00000575372.5 | c.153G>A | p.Pro51= | synonymous_variant | 2/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152232Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00144 AC: 345AN: 238964Hom.: 5 AF XY: 0.00193 AC XY: 251AN XY: 129796
GnomAD4 exome AF: 0.000643 AC: 931AN: 1447756Hom.: 16 Cov.: 31 AF XY: 0.000907 AC XY: 652AN XY: 718590
GnomAD4 genome ? AF: 0.000335 AC: 51AN: 152350Hom.: 1 Cov.: 32 AF XY: 0.000537 AC XY: 40AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at