7-3301728-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152744.4(SDK1):c.142C>A(p.Pro48Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00505 in 977,352 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152744.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDK1 | ENST00000404826.7 | c.142C>A | p.Pro48Thr | missense_variant | Exon 1 of 45 | 1 | NM_152744.4 | ENSP00000385899.2 | ||
SDK1 | ENST00000389531.7 | c.142C>A | p.Pro48Thr | missense_variant | Exon 1 of 44 | 5 | ENSP00000374182.3 | |||
SDK1-AS1 | ENST00000437354.1 | n.224+501G>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0224 AC: 3258AN: 145166Hom.: 130 Cov.: 29
GnomAD4 exome AF: 0.00201 AC: 1674AN: 832150Hom.: 65 Cov.: 28 AF XY: 0.00189 AC XY: 727AN XY: 384350
GnomAD4 genome AF: 0.0225 AC: 3262AN: 145202Hom.: 130 Cov.: 29 AF XY: 0.0216 AC XY: 1523AN XY: 70590
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.142C>A (p.P48T) alteration is located in exon 1 (coding exon 1) of the SDK1 gene. This alteration results from a C to A substitution at nucleotide position 142, causing the proline (P) at amino acid position 48 to be replaced by a threonine (T). 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