X-63350707-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001012968.3(SPIN4):c.113G>A(p.Arg38Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000273 in 1,098,003 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012968.3 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 |
---|---|---|---|---|---|---|---|
SPIN4 | NM_001012968.3 | c.113G>A | p.Arg38Lys | missense_variant | 1/1 | ENST00000374884.3 | |
SPIN4-AS1 | NR_046739.1 | n.298+973C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPIN4 | ENST00000374884.3 | c.113G>A | p.Arg38Lys | missense_variant | 1/1 | NM_001012968.3 | P1 | ||
SPIN4-AS1 | ENST00000451979.1 | n.89+973C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
LINC01278 | ENST00000667050.1 | n.407+49074G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 111839Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34009 FAILED QC
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1098003Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363363
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 111890Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34070
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.113G>A (p.R38K) alteration is located in exon 1 (coding exon 1) of the SPIN4 gene. This alteration results from a G to A substitution at nucleotide position 113, causing the arginine (R) at amino acid position 38 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