7-11406947-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015204.3(THSD7A):c.4025G>A(p.Arg1342Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000998 in 1,613,794 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_015204.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THSD7A | ENST00000423059.9 | c.4025G>A | p.Arg1342Gln | missense_variant | Exon 21 of 28 | 5 | NM_015204.3 | ENSP00000406482.2 | ||
ENSG00000230333 | ENST00000445839.5 | n.441+23039C>T | intron_variant | Intron 3 of 3 | 4 | |||||
ENSG00000230435 | ENST00000425837.1 | n.-8C>T | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00474 AC: 721AN: 152114Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00142 AC: 353AN: 248726Hom.: 3 AF XY: 0.00106 AC XY: 143AN XY: 134942
GnomAD4 exome AF: 0.000608 AC: 889AN: 1461562Hom.: 4 Cov.: 31 AF XY: 0.000576 AC XY: 419AN XY: 727054
GnomAD4 genome AF: 0.00474 AC: 722AN: 152232Hom.: 5 Cov.: 32 AF XY: 0.00450 AC XY: 335AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at