17-7631215-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001040.5(SHBG):c.409G>A(p.Glu137Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000165 in 1,575,670 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040.5 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 |
---|---|---|---|---|---|---|---|
SHBG | NM_001040.5 | c.409G>A | p.Glu137Lys | missense_variant | 4/8 | ENST00000380450.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHBG | ENST00000380450.9 | c.409G>A | p.Glu137Lys | missense_variant | 4/8 | 1 | NM_001040.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152152Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00000510 AC: 1AN: 196016Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 105572
GnomAD4 exome AF: 0.00000773 AC: 11AN: 1423518Hom.: 0 Cov.: 32 AF XY: 0.00000142 AC XY: 1AN XY: 704986
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152152Hom.: 1 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.409G>A (p.E137K) alteration is located in exon 4 (coding exon 4) of the SHBG gene. This alteration results from a G to A substitution at nucleotide position 409, causing the glutamic acid (E) at amino acid position 137 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