9-14737508-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001379081.2(FREM1):āc.6428A>Cā(p.Gln2143Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,612,218 control chromosomes in the GnomAD database, including 431,661 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001379081.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FREM1 | NM_001379081.2 | c.6428A>C | p.Gln2143Pro | missense_variant | Exon 37 of 37 | ENST00000380880.4 | NP_001366010.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.747 AC: 113483AN: 151860Hom.: 42495 Cov.: 31
GnomAD3 exomes AF: 0.735 AC: 181690AN: 247034Hom.: 66949 AF XY: 0.731 AC XY: 98028AN XY: 134044
GnomAD4 exome AF: 0.729 AC: 1064555AN: 1460238Hom.: 389145 Cov.: 43 AF XY: 0.727 AC XY: 528254AN XY: 726350
GnomAD4 genome AF: 0.747 AC: 113560AN: 151980Hom.: 42516 Cov.: 31 AF XY: 0.745 AC XY: 55341AN XY: 74276
ClinVar
Submissions by phenotype
not specified Benign:3
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Oculotrichoanal syndrome Benign:3
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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. -
not provided Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at