X-18256860-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006089.3(SCML2):āc.1444A>Gā(p.Lys482Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000075 in 1,067,368 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. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006089.3 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 |
---|---|---|---|---|---|---|---|
SCML2 | NM_006089.3 | c.1444A>G | p.Lys482Glu | missense_variant | 11/15 | ENST00000251900.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCML2 | ENST00000251900.9 | c.1444A>G | p.Lys482Glu | missense_variant | 11/15 | 1 | NM_006089.3 | P1 | |
SCML2 | ENST00000665583.1 | c.652A>G | p.Lys218Glu | missense_variant | 5/8 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 0.00000750 AC: 8AN: 1067368Hom.: 0 Cov.: 28 AF XY: 0.00000582 AC XY: 2AN XY: 343656
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2022 | The c.1444A>G (p.K482E) alteration is located in exon 11 (coding exon 10) of the SCML2 gene. This alteration results from a A to G substitution at nucleotide position 1444, causing the lysine (K) at amino acid position 482 to be replaced by a glutamic acid (E). 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
Publications
No publications associated with this variant yet.