chr7-3301678-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152744.4(SDK1):c.92C>T(p.Ser31Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000308 in 974,156 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S31Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_152744.4 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 |
---|---|---|---|---|---|---|---|
SDK1 | NM_152744.4 | c.92C>T | p.Ser31Phe | missense_variant | 1/45 | ENST00000404826.7 | |
SDK1-AS1 | XR_001744897.3 | n.49857+551G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDK1 | ENST00000404826.7 | c.92C>T | p.Ser31Phe | missense_variant | 1/45 | 1 | NM_152744.4 | P2 | |
SDK1-AS1 | ENST00000437354.1 | n.224+551G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
SDK1 | ENST00000389531.7 | c.92C>T | p.Ser31Phe | missense_variant | 1/44 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000138 AC: 2AN: 144458Hom.: 0 Cov.: 29
GnomAD4 exome AF: 0.00000121 AC: 1AN: 829698Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 383278
GnomAD4 genome ? AF: 0.0000138 AC: 2AN: 144458Hom.: 0 Cov.: 29 AF XY: 0.0000142 AC XY: 1AN XY: 70208
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.92C>T (p.S31F) alteration is located in exon 1 (coding exon 1) of the SDK1 gene. This alteration results from a C to T substitution at nucleotide position 92, causing the serine (S) at amino acid position 31 to be replaced by a phenylalanine (F). 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