chrX-66022315-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007268.3(VSIG4):c.1148C>T(p.Thr383Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00836 in 1,211,201 control chromosomes in the GnomAD database, including 26 homozygotes. There are 3,139 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_007268.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VSIG4 | NM_007268.3 | c.1148C>T | p.Thr383Ile | missense_variant | 8/8 | ENST00000374737.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSIG4 | ENST00000374737.9 | c.1148C>T | p.Thr383Ile | missense_variant | 8/8 | 1 | NM_007268.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00516 AC: 584AN: 113099Hom.: 0 Cov.: 24 AF XY: 0.00417 AC XY: 147AN XY: 35231
GnomAD3 exomes AF: 0.00559 AC: 1021AN: 182568Hom.: 6 AF XY: 0.00578 AC XY: 389AN XY: 67344
GnomAD4 exome AF: 0.00869 AC: 9538AN: 1098048Hom.: 26 Cov.: 31 AF XY: 0.00823 AC XY: 2992AN XY: 363468
GnomAD4 genome AF: 0.00516 AC: 584AN: 113153Hom.: 0 Cov.: 24 AF XY: 0.00416 AC XY: 147AN XY: 35295
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at