8-6621465-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_024596.5(MCPH1):c.2226C>T(p.Ser742Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,609,454 control chromosomes in the GnomAD database, including 139,190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024596.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.403 AC: 61191AN: 151902Hom.: 12645 Cov.: 33
GnomAD3 exomes AF: 0.428 AC: 106400AN: 248850Hom.: 23588 AF XY: 0.430 AC XY: 58060AN XY: 135078
GnomAD4 exome AF: 0.412 AC: 600865AN: 1457434Hom.: 126529 Cov.: 47 AF XY: 0.415 AC XY: 300822AN XY: 725226
GnomAD4 genome AF: 0.403 AC: 61245AN: 152020Hom.: 12661 Cov.: 33 AF XY: 0.408 AC XY: 30340AN XY: 74296
ClinVar
Submissions by phenotype
not specified Benign:4
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Microcephaly 1, primary, autosomal recessive Benign:4
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not provided Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at