rs61734132
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001164665.2(KIAA1549):āc.1940C>Gā(p.Ser647Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0652 in 1,609,428 control chromosomes in the GnomAD database, including 3,863 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001164665.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA1549 | NM_001164665.2 | c.1940C>G | p.Ser647Cys | missense_variant | 2/20 | ENST00000422774.2 | |
KIAA1549 | NM_020910.3 | c.1940C>G | p.Ser647Cys | missense_variant | 2/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1549 | ENST00000422774.2 | c.1940C>G | p.Ser647Cys | missense_variant | 2/20 | 1 | NM_001164665.2 | A2 | |
KIAA1549 | ENST00000440172.5 | c.1940C>G | p.Ser647Cys | missense_variant | 2/20 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0551 AC: 8379AN: 152128Hom.: 286 Cov.: 32
GnomAD3 exomes AF: 0.0631 AC: 15129AN: 239650Hom.: 612 AF XY: 0.0680 AC XY: 8835AN XY: 129834
GnomAD4 exome AF: 0.0663 AC: 96563AN: 1457182Hom.: 3577 Cov.: 49 AF XY: 0.0685 AC XY: 49613AN XY: 724218
GnomAD4 genome ? AF: 0.0550 AC: 8378AN: 152246Hom.: 286 Cov.: 32 AF XY: 0.0552 AC XY: 4109AN XY: 74436
ClinVar
Submissions by phenotype
Retinitis pigmentosa 86 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at