9-136402825-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001039707.2(ENTR1):āc.1271G>Cā(p.Arg424Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000245 in 1,613,174 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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. R424K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001039707.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENTR1 | NM_001039707.2 | c.1271G>C | p.Arg424Thr | missense_variant | 10/10 | ENST00000357365.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENTR1 | ENST00000357365.8 | c.1271G>C | p.Arg424Thr | missense_variant | 10/10 | 5 | NM_001039707.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000987 AC: 15AN: 151928Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000161 AC: 40AN: 248498Hom.: 1 AF XY: 0.000178 AC XY: 24AN XY: 135138
GnomAD4 exome AF: 0.000260 AC: 380AN: 1461128Hom.: 1 Cov.: 31 AF XY: 0.000246 AC XY: 179AN XY: 726836
GnomAD4 genome ? AF: 0.0000987 AC: 15AN: 152046Hom.: 0 Cov.: 29 AF XY: 0.000108 AC XY: 8AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.1271G>C (p.R424T) alteration is located in exon 10 (coding exon 10) of the SDCCAG3 gene. This alteration results from a G to C substitution at nucleotide position 1271, causing the arginine (R) at amino acid position 424 to be replaced by a threonine (T). 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