X-18265730-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006089.3(SCML2):c.803C>T(p.Pro268Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000177 in 1,208,454 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 62 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006089.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000809 AC: 9AN: 111216Hom.: 0 Cov.: 22 AF XY: 0.0000598 AC XY: 2AN XY: 33418
GnomAD3 exomes AF: 0.000115 AC: 21AN: 183317Hom.: 0 AF XY: 0.0000738 AC XY: 5AN XY: 67789
GnomAD4 exome AF: 0.000187 AC: 205AN: 1097238Hom.: 0 Cov.: 29 AF XY: 0.000165 AC XY: 60AN XY: 362634
GnomAD4 genome AF: 0.0000809 AC: 9AN: 111216Hom.: 0 Cov.: 22 AF XY: 0.0000598 AC XY: 2AN XY: 33418
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.803C>T (p.P268L) alteration is located in exon 8 (coding exon 7) of the SCML2 gene. This alteration results from a C to T substitution at nucleotide position 803, causing the proline (P) at amino acid position 268 to be replaced by a leucine (L). 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