chr5-141644605-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033449.3(FCHSD1):c.1610A>G(p.Asp537Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033449.3 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 |
---|---|---|---|---|---|---|---|
FCHSD1 | NM_033449.3 | c.1610A>G | p.Asp537Gly | missense_variant | 16/20 | ENST00000435817.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCHSD1 | ENST00000435817.7 | c.1610A>G | p.Asp537Gly | missense_variant | 16/20 | 1 | NM_033449.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 249214Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135202
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461686Hom.: 0 Cov.: 33 AF XY: 0.0000701 AC XY: 51AN XY: 727132
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.1610A>G (p.D537G) alteration is located in exon 16 (coding exon 16) of the FCHSD1 gene. This alteration results from a A to G substitution at nucleotide position 1610, causing the aspartic acid (D) at amino acid position 537 to be replaced by a glycine (G). 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