NM_080860.4:c.733G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_080860.4(RSPH1):c.733G>A(p.Gly245Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00571 in 1,613,710 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_080860.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RSPH1 | NM_080860.4 | c.733G>A | p.Gly245Arg | missense_variant | Exon 8 of 9 | ENST00000291536.8 | NP_543136.1 | |
RSPH1 | NM_001286506.2 | c.619G>A | p.Gly207Arg | missense_variant | Exon 7 of 8 | NP_001273435.1 | ||
RSPH1 | XM_011529786.2 | c.661G>A | p.Gly221Arg | missense_variant | Exon 7 of 8 | XP_011528088.1 | ||
RSPH1 | XM_005261208.3 | c.526G>A | p.Gly176Arg | missense_variant | Exon 6 of 7 | XP_005261265.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RSPH1 | ENST00000291536.8 | c.733G>A | p.Gly245Arg | missense_variant | Exon 8 of 9 | 1 | NM_080860.4 | ENSP00000291536.3 | ||
RSPH1 | ENST00000398352.3 | c.619G>A | p.Gly207Arg | missense_variant | Exon 7 of 8 | 5 | ENSP00000381395.3 | |||
RSPH1 | ENST00000493019.1 | n.2351G>A | non_coding_transcript_exon_variant | Exon 7 of 8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00450 AC: 683AN: 151850Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.00385 AC: 967AN: 251258Hom.: 5 AF XY: 0.00378 AC XY: 513AN XY: 135802
GnomAD4 exome AF: 0.00583 AC: 8524AN: 1461742Hom.: 31 Cov.: 32 AF XY: 0.00567 AC XY: 4122AN XY: 727172
GnomAD4 genome AF: 0.00449 AC: 683AN: 151968Hom.: 1 Cov.: 30 AF XY: 0.00409 AC XY: 304AN XY: 74268
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at