chr2-137057149-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001316349.2(THSD7B):c.869C>T(p.Ser290Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00047 in 1,613,882 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001316349.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THSD7B | NM_001316349.2 | c.869C>T | p.Ser290Leu | missense_variant | 3/28 | ENST00000409968.6 | |
THSD7B | XM_047445935.1 | c.446C>T | p.Ser149Leu | missense_variant | 3/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THSD7B | ENST00000409968.6 | c.869C>T | p.Ser290Leu | missense_variant | 3/28 | 5 | NM_001316349.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000217 AC: 54AN: 248926Hom.: 0 AF XY: 0.000244 AC XY: 33AN XY: 135084
GnomAD4 exome AF: 0.000506 AC: 740AN: 1461684Hom.: 1 Cov.: 34 AF XY: 0.000517 AC XY: 376AN XY: 727124
GnomAD4 genome AF: 0.000125 AC: 19AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2022 | The c.776C>T (p.S259L) alteration is located in exon 2 (coding exon 2) of the THSD7B gene. This alteration results from a C to T substitution at nucleotide position 776, causing the serine (S) at amino acid position 259 to be replaced by a leucine (L). 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