6-158999542-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_031924.8(RSPH3):c.9A>C(p.Ser3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000188 in 1,598,516 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 (★). Synonymous variant affecting the same amino acid position (i.e. S3S) has been classified as Benign.
Frequency
Consequence
NM_031924.8 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPH3 | NM_031924.8 | c.9A>C | p.Ser3= | synonymous_variant | 1/8 | ENST00000367069.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPH3 | ENST00000367069.7 | c.9A>C | p.Ser3= | synonymous_variant | 1/8 | 1 | NM_031924.8 | P1 | |
RSPH3 | ENST00000449822.5 | c.9A>C | p.Ser3= | synonymous_variant | 1/6 | 2 | |||
TAGAP-AS1 | ENST00000607391.5 | n.236+8970T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151318Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000410 AC: 1AN: 243884Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131498
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1447198Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 717550
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151318Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73854
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 32 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 02, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at