chr3-120409570-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007085.5(FSTL1):c.424G>A(p.Gly142Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007085.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FSTL1 | NM_007085.5 | c.424G>A | p.Gly142Ser | missense_variant | Exon 6 of 11 | ENST00000295633.8 | NP_009016.1 | |
BTNL12P | NR_187254.1 | n.997-6231C>T | intron_variant | Intron 3 of 4 | ||||
BTNL12P | NR_187255.1 | n.997-6231C>T | intron_variant | Intron 3 of 4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251466Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135906
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461666Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727156
GnomAD4 genome AF: 0.000315 AC: 48AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.424G>A (p.G142S) alteration is located in exon 6 (coding exon 5) of the FSTL1 gene. This alteration results from a G to A substitution at nucleotide position 424, causing the glycine (G) at amino acid position 142 to be replaced by a serine (S). 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