rs10961689
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001379081.2(FREM1):c.6428A>T(p.Gln2143Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q2143P) has been classified as Benign.
Frequency
Consequence
NM_001379081.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FREM1 | NM_001379081.2 | c.6428A>T | p.Gln2143Leu | missense_variant | 37/37 | ENST00000380880.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM1 | ENST00000380880.4 | c.6428A>T | p.Gln2143Leu | missense_variant | 37/37 | 5 | NM_001379081.2 | P1 | |
FREM1 | ENST00000380894.5 | c.2036A>T | p.Gln679Leu | missense_variant | 14/14 | 1 | |||
FREM1 | ENST00000380875.7 | c.*994A>T | 3_prime_UTR_variant, NMD_transcript_variant | 31/31 | 1 | ||||
FREM1 | ENST00000427623.5 | c.*609A>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151932Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000810 AC: 2AN: 247034Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134044
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460618Hom.: 0 Cov.: 43 AF XY: 0.00000138 AC XY: 1AN XY: 726522
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151932Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74182
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at