chrX-17745535-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001037540.3(SCML1):āc.113A>Gā(p.Asn38Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000456 in 1,096,440 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001037540.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCML1 | NM_001037540.3 | c.113A>G | p.Asn38Ser | missense_variant | 3/8 | ENST00000380041.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCML1 | ENST00000380041.8 | c.113A>G | p.Asn38Ser | missense_variant | 3/8 | 5 | NM_001037540.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000890 AC: 1AN: 112330Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34502
GnomAD3 exomes AF: 0.0000123 AC: 2AN: 162521Hom.: 0 AF XY: 0.0000195 AC XY: 1AN XY: 51281
GnomAD4 exome AF: 0.00000406 AC: 4AN: 984110Hom.: 0 Cov.: 17 AF XY: 0.00000716 AC XY: 2AN XY: 279234
GnomAD4 genome ? AF: 0.00000890 AC: 1AN: 112330Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.113A>G (p.N38S) alteration is located in exon 3 (coding exon 2) of the SCML1 gene. This alteration results from a A to G substitution at nucleotide position 113, causing the asparagine (N) at amino acid position 38 to be replaced by a serine (S). 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