chr3-120396974-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_007085.5(FSTL1):āc.905G>Cā(p.Arg302Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000422 in 1,612,412 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 (ā ).
Frequency
Consequence
NM_007085.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FSTL1 | NM_007085.5 | c.905G>C | p.Arg302Thr | missense_variant | 11/11 | ENST00000295633.8 | |
LRRC58-DT | XR_007096031.1 | n.964-18827C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FSTL1 | ENST00000295633.8 | c.905G>C | p.Arg302Thr | missense_variant | 11/11 | 1 | NM_007085.5 | P1 | |
ENST00000494869.2 | n.633-18827C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251272Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135800
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1460100Hom.: 0 Cov.: 28 AF XY: 0.0000551 AC XY: 40AN XY: 726494
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.905G>C (p.R302T) alteration is located in exon 11 (coding exon 10) of the FSTL1 gene. This alteration results from a G to C substitution at nucleotide position 905, causing the arginine (R) at amino acid position 302 to be replaced by a threonine (T). 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