chr1-32889021-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002143.3(HPCA):āc.123A>Gā(p.Gly41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_002143.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPCA | NM_002143.3 | c.123A>G | p.Gly41= | synonymous_variant | 2/4 | ENST00000373467.4 | |
HPCA | XM_005270792.4 | c.123A>G | p.Gly41= | synonymous_variant | 2/4 | ||
HPCA | XM_017001118.3 | c.123A>G | p.Gly41= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPCA | ENST00000373467.4 | c.123A>G | p.Gly41= | synonymous_variant | 2/4 | 1 | NM_002143.3 | P1 | |
HPCA | ENST00000480118.5 | n.182A>G | non_coding_transcript_exon_variant | 2/3 | 5 | ||||
HPCA | ENST00000459874.5 | n.54+2506A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
HPCA | ENST00000470166.5 | n.126+2902A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.