chr15-71215207-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_024817.3(THSD4):āc.272A>Gā(p.Gln91Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000808 in 1,361,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024817.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THSD4 | NM_024817.3 | c.272A>G | p.Gln91Arg | missense_variant | 4/18 | ENST00000261862.8 | |
THSD4 | NM_001394532.1 | c.272A>G | p.Gln91Arg | missense_variant | 4/18 | ||
THSD4 | XM_047433080.1 | c.272A>G | p.Gln91Arg | missense_variant | 4/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THSD4 | ENST00000261862.8 | c.272A>G | p.Gln91Arg | missense_variant | 4/18 | 5 | NM_024817.3 | P1 | |
THSD4 | ENST00000355327.7 | c.272A>G | p.Gln91Arg | missense_variant | 4/18 | 5 | P1 | ||
THSD4 | ENST00000620694.1 | c.272A>G | p.Gln91Arg | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000528 AC: 8AN: 151418Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000248 AC: 3AN: 1210480Hom.: 0 Cov.: 31 AF XY: 0.00000169 AC XY: 1AN XY: 592058
GnomAD4 genome AF: 0.0000528 AC: 8AN: 151418Hom.: 0 Cov.: 33 AF XY: 0.0000406 AC XY: 3AN XY: 73920
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.272A>G (p.Q91R) alteration is located in exon 3 (coding exon 3) of the THSD4 gene. This alteration results from a A to G substitution at nucleotide position 272, causing the glutamine (Q) at amino acid position 91 to be replaced by an arginine (R). 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