19-45766698-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_175875.5(SIX5):c.1261G>A(p.Val421Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000652 in 1,532,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V421V) has been classified as Likely benign.
Frequency
Consequence
NM_175875.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIX5 | NM_175875.5 | c.1261G>A | p.Val421Ile | missense_variant | 2/3 | ENST00000317578.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIX5 | ENST00000317578.7 | c.1261G>A | p.Val421Ile | missense_variant | 2/3 | 1 | NM_175875.5 | P1 | |
ENST00000559756.1 | n.1180+734C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
SIX5 | ENST00000560168.1 | c.*449G>A | 3_prime_UTR_variant | 3/3 | 4 | ||||
SIX5 | ENST00000560160.1 | c.587-587G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000221 AC: 3AN: 136030Hom.: 0 AF XY: 0.0000133 AC XY: 1AN XY: 75178
GnomAD4 exome AF: 0.00000579 AC: 8AN: 1380664Hom.: 0 Cov.: 33 AF XY: 0.00000441 AC XY: 3AN XY: 680584
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
Branchiootorenal syndrome 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at