chr2-137095054-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.1132G>A(p.Glu378Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,744 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
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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.1132G>A | p.Glu378Lys | missense_variant | 4/28 | ENST00000409968.6 | |
THSD7B | XM_047445935.1 | c.709G>A | p.Glu237Lys | missense_variant | 4/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THSD7B | ENST00000409968.6 | c.1132G>A | p.Glu378Lys | missense_variant | 4/28 | 5 | NM_001316349.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248954Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135056
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461554Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727054
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.1039G>A (p.E347K) alteration is located in exon 3 (coding exon 3) of the THSD7B gene. This alteration results from a G to A substitution at nucleotide position 1039, causing the glutamic acid (E) at amino acid position 347 to be replaced by a lysine (K). 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