chr4-75950758-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018115.4(SDAD1):c.2056A>G(p.Met686Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000314 in 1,592,466 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_018115.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDAD1 | NM_018115.4 | c.2056A>G | p.Met686Val | missense_variant | 22/22 | ENST00000356260.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDAD1 | ENST00000356260.10 | c.2056A>G | p.Met686Val | missense_variant | 22/22 | 1 | NM_018115.4 | P1 | |
SDAD1 | ENST00000395710.5 | c.*1912A>G | 3_prime_UTR_variant, NMD_transcript_variant | 22/22 | 1 | ||||
SDAD1 | ENST00000395711.8 | c.1945A>G | p.Met649Val | missense_variant | 21/21 | 2 | |||
SDAD1 | ENST00000502543.5 | n.249A>G | non_coding_transcript_exon_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1440302Hom.: 0 Cov.: 27 AF XY: 0.00000140 AC XY: 1AN XY: 715008
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.2056A>G (p.M686V) alteration is located in exon 22 (coding exon 22) of the SDAD1 gene. This alteration results from a A to G substitution at nucleotide position 2056, causing the methionine (M) at amino acid position 686 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