chr4-143695586-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001168235.2(FREM3):c.5090A>C(p.His1697Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 1,537,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001168235.2 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 |
---|---|---|---|---|---|---|---|
FREM3 | NM_001168235.2 | c.5090A>C | p.His1697Pro | missense_variant | 1/8 | ENST00000329798.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM3 | ENST00000329798.5 | c.5090A>C | p.His1697Pro | missense_variant | 1/8 | 5 | NM_001168235.2 | P1 | |
GUSBP5 | ENST00000641328.1 | n.862-43389T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000140 AC: 2AN: 142460Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 76162
GnomAD4 exome AF: 0.0000173 AC: 24AN: 1385044Hom.: 0 Cov.: 32 AF XY: 0.0000146 AC XY: 10AN XY: 683438
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.5090A>C (p.H1697P) alteration is located in exon 1 (coding exon 1) of the FREM3 gene. This alteration results from a A to C substitution at nucleotide position 5090, causing the histidine (H) at amino acid position 1697 to be replaced by a proline (P). 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