chr1-48359748-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019073.4(SPATA6):c.932G>A(p.Arg311Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,612,772 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_019073.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA6 | NM_019073.4 | c.932G>A | p.Arg311Lys | missense_variant | 10/13 | ENST00000371847.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA6 | ENST00000371847.8 | c.932G>A | p.Arg311Lys | missense_variant | 10/13 | 1 | NM_019073.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249892Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135140
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460532Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726548
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152240Hom.: 1 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.932G>A (p.R311K) alteration is located in exon 10 (coding exon 10) of the SPATA6 gene. This alteration results from a G to A substitution at nucleotide position 932, causing the arginine (R) at amino acid position 311 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at