chr4-143695505-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001168235.2(FREM3):c.5171G>A(p.Arg1724Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000677 in 1,537,048 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. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FREM3 | NM_001168235.2 | c.5171G>A | p.Arg1724Gln | missense_variant | 1/8 | ENST00000329798.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM3 | ENST00000329798.5 | c.5171G>A | p.Arg1724Gln | missense_variant | 1/8 | 5 | NM_001168235.2 | P1 | |
GUSBP5 | ENST00000641328.1 | n.862-43470C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000840 AC: 12AN: 142900Hom.: 0 AF XY: 0.0000789 AC XY: 6AN XY: 76044
GnomAD4 exome AF: 0.0000708 AC: 98AN: 1384862Hom.: 0 Cov.: 32 AF XY: 0.0000615 AC XY: 42AN XY: 683328
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | The c.5171G>A (p.R1724Q) alteration is located in exon 1 (coding exon 1) of the FREM3 gene. This alteration results from a G to A substitution at nucleotide position 5171, causing the arginine (R) at amino acid position 1724 to be replaced by a glutamine (Q). 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