chr6-158977771-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_031924.8(RSPH3):c.1024G>A(p.Glu342Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 1,614,090 control chromosomes in the GnomAD database, including 421 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_031924.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RSPH3 | ENST00000367069.7 | c.1024G>A | p.Glu342Lys | missense_variant | Exon 8 of 8 | 1 | NM_031924.8 | ENSP00000356036.1 | ||
RSPH3 | ENST00000449822.5 | c.736G>A | p.Glu246Lys | missense_variant | Exon 6 of 6 | 2 | ENSP00000393195.1 |
Frequencies
GnomAD3 genomes AF: 0.0179 AC: 2716AN: 152152Hom.: 34 Cov.: 32
GnomAD3 exomes AF: 0.0168 AC: 4213AN: 251332Hom.: 45 AF XY: 0.0171 AC XY: 2323AN XY: 135848
GnomAD4 exome AF: 0.0217 AC: 31768AN: 1461820Hom.: 387 Cov.: 32 AF XY: 0.0213 AC XY: 15519AN XY: 727222
GnomAD4 genome AF: 0.0178 AC: 2718AN: 152270Hom.: 34 Cov.: 32 AF XY: 0.0174 AC XY: 1293AN XY: 74454
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 32 Benign:2
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not provided Benign:2
See Variant Classification Assertion Criteria. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at