chr12-108196038-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014653.4(WSCD2):c.206A>T(p.Asp69Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,614,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014653.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WSCD2 | NM_014653.4 | c.206A>T | p.Asp69Val | missense_variant | 2/9 | ENST00000547525.6 | |
LOC124903077 | XR_007063583.1 | n.183-5019T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WSCD2 | ENST00000547525.6 | c.206A>T | p.Asp69Val | missense_variant | 2/9 | 1 | NM_014653.4 | P1 | |
WSCD2 | ENST00000332082.8 | c.206A>T | p.Asp69Val | missense_variant | 3/10 | 1 | P1 | ||
WSCD2 | ENST00000549903.1 | c.206A>T | p.Asp69Val | missense_variant | 1/9 | 5 | |||
WSCD2 | ENST00000551638.5 | c.-77-10251A>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249452Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135340
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461892Hom.: 0 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 727246
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.206A>T (p.D69V) alteration is located in exon 2 (coding exon 1) of the WSCD2 gene. This alteration results from a A to T substitution at nucleotide position 206, causing the aspartic acid (D) at amino acid position 69 to be replaced by a valine (V). 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