9-14737248-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001379081.2(FREM1):c.*148A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 567,020 control chromosomes in the GnomAD database, including 351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001379081.2 3_prime_UTR
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.*148A>G | 3_prime_UTR_variant | Exon 37 of 37 | ENST00000380880.4 | NP_001366010.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FREM1 | ENST00000380880 | c.*148A>G | 3_prime_UTR_variant | Exon 37 of 37 | 5 | NM_001379081.2 | ENSP00000370262.3 | |||
FREM1 | ENST00000380894 | c.*148A>G | 3_prime_UTR_variant | Exon 14 of 14 | 1 | ENSP00000370278.1 | ||||
FREM1 | ENST00000380875.7 | n.*1254A>G | non_coding_transcript_exon_variant | Exon 31 of 31 | 1 | ENSP00000370257.3 | ||||
FREM1 | ENST00000380875.7 | n.*1254A>G | 3_prime_UTR_variant | Exon 31 of 31 | 1 | ENSP00000370257.3 |
Frequencies
GnomAD3 genomes AF: 0.0340 AC: 5175AN: 152154Hom.: 277 Cov.: 32
GnomAD4 exome AF: 0.00409 AC: 1698AN: 414748Hom.: 74 Cov.: 5 AF XY: 0.00341 AC XY: 731AN XY: 214528
GnomAD4 genome AF: 0.0340 AC: 5170AN: 152272Hom.: 277 Cov.: 32 AF XY: 0.0326 AC XY: 2429AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:2
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Oculotrichoanal syndrome Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at