chr13-24223347-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001166271.3(SPATA13):āc.418T>Gā(p.Ser140Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,551,368 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S140L) has been classified as Likely benign.
Frequency
Consequence
NM_001166271.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA13 | NM_001166271.3 | c.418T>G | p.Ser140Ala | missense_variant | 2/13 | ENST00000382108.8 | |
SPATA13 | NM_001286792.2 | c.604T>G | p.Ser202Ala | missense_variant | 4/15 | ||
SPATA13 | NM_153023.4 | c.-222-26130T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.418T>G | p.Ser140Ala | missense_variant | 2/13 | 5 | NM_001166271.3 | ||
SPATA13 | ENST00000424834.6 | c.418T>G | p.Ser140Ala | missense_variant | 4/15 | 1 | |||
SPATA13 | ENST00000382095.8 | c.-222-26130T>G | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.740T>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000128 AC: 20AN: 156020Hom.: 0 AF XY: 0.0000967 AC XY: 8AN XY: 82772
GnomAD4 exome AF: 0.000234 AC: 327AN: 1399106Hom.: 0 Cov.: 30 AF XY: 0.000223 AC XY: 154AN XY: 690078
GnomAD4 genome AF: 0.000236 AC: 36AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.418T>G (p.S140A) alteration is located in exon 2 (coding exon 1) of the SPATA13 gene. This alteration results from a T to G substitution at nucleotide position 418, causing the serine (S) at amino acid position 140 to be replaced by an alanine (A). 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