chr2-137170920-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001316349.2(THSD7B):c.1705G>A(p.Val569Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,612,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THSD7B | NM_001316349.2 | c.1705G>A | p.Val569Ile | missense_variant | 7/28 | ENST00000409968.6 | |
THSD7B | XM_047445935.1 | c.1282G>A | p.Val428Ile | missense_variant | 7/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THSD7B | ENST00000409968.6 | c.1705G>A | p.Val569Ile | missense_variant | 7/28 | 5 | NM_001316349.2 | P1 | |
THSD7B | ENST00000485379.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000564 AC: 14AN: 248280Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134694
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1460364Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 726430
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.1612G>A (p.V538I) alteration is located in exon 6 (coding exon 6) of the THSD7B gene. This alteration results from a G to A substitution at nucleotide position 1612, causing the valine (V) at amino acid position 538 to be replaced by an isoleucine (I). 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