chr3-69181696-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015123.3(FRMD4B):c.2054C>G(p.Ser685Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000734 in 1,610,782 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015123.3 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 |
---|---|---|---|---|---|---|---|
FRMD4B | NM_015123.3 | c.2054C>G | p.Ser685Cys | missense_variant | 21/23 | ENST00000398540.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMD4B | ENST00000398540.8 | c.2054C>G | p.Ser685Cys | missense_variant | 21/23 | 1 | NM_015123.3 | P1 | |
FRMD4B | ENST00000478263.5 | c.1010C>G | p.Ser337Cys | missense_variant | 11/13 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000552 AC: 84AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000567 AC: 138AN: 243484Hom.: 0 AF XY: 0.000544 AC XY: 72AN XY: 132248
GnomAD4 exome AF: 0.000753 AC: 1098AN: 1458506Hom.: 1 Cov.: 32 AF XY: 0.000750 AC XY: 544AN XY: 725372
GnomAD4 genome ? AF: 0.000552 AC: 84AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 29AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.2054C>G (p.S685C) alteration is located in exon 21 (coding exon 21) of the FRMD4B gene. This alteration results from a C to G substitution at nucleotide position 2054, causing the serine (S) at amino acid position 685 to be replaced by a cysteine (C). 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