X-18324029-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006089.3(SCML2):c.227A>G(p.Asn76Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000463 in 1,209,076 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 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
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000360 AC: 4AN: 111202Hom.: 0 Cov.: 22 AF XY: 0.0000599 AC XY: 2AN XY: 33384
GnomAD3 exomes AF: 0.000213 AC: 39AN: 183442Hom.: 0 AF XY: 0.000147 AC XY: 10AN XY: 67880
GnomAD4 exome AF: 0.0000474 AC: 52AN: 1097874Hom.: 0 Cov.: 30 AF XY: 0.0000440 AC XY: 16AN XY: 363232
GnomAD4 genome AF: 0.0000360 AC: 4AN: 111202Hom.: 0 Cov.: 22 AF XY: 0.0000599 AC XY: 2AN XY: 33384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.227A>G (p.N76S) alteration is located in exon 5 (coding exon 4) of the SCML2 gene. This alteration results from a A to G substitution at nucleotide position 227, causing the asparagine (N) at amino acid position 76 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