chrX-11120925-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005333.5(HCCS):āc.540A>Gā(p.Pro180=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,206,230 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P180P) has been classified as Likely benign.
Frequency
Consequence
NM_005333.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCCS | NM_005333.5 | c.540A>G | p.Pro180= | synonymous_variant | 6/7 | ENST00000380762.5 | |
HCCS | NM_001122608.3 | c.540A>G | p.Pro180= | synonymous_variant | 6/7 | ||
HCCS | NM_001171991.3 | c.540A>G | p.Pro180= | synonymous_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCCS | ENST00000380762.5 | c.540A>G | p.Pro180= | synonymous_variant | 6/7 | 1 | NM_005333.5 | P1 | |
HCCS | ENST00000380763.7 | c.540A>G | p.Pro180= | synonymous_variant | 6/7 | 1 | P1 | ||
HCCS | ENST00000321143.8 | c.540A>G | p.Pro180= | synonymous_variant | 6/7 | 2 | P1 | ||
ARHGAP6 | ENST00000657361.1 | c.1733-880T>C | intron_variant | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000356 AC: 4AN: 112480Hom.: 0 Cov.: 23 AF XY: 0.0000578 AC XY: 2AN XY: 34618
GnomAD4 exome AF: 0.00000823 AC: 9AN: 1093750Hom.: 0 Cov.: 29 AF XY: 0.00000835 AC XY: 3AN XY: 359224
GnomAD4 genome AF: 0.0000356 AC: 4AN: 112480Hom.: 0 Cov.: 23 AF XY: 0.0000578 AC XY: 2AN XY: 34618
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 25, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at