4-173391386-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007281.4(SCRG1):āc.29T>Cā(p.Ile10Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000124 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007281.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCRG1 | NM_007281.4 | c.29T>C | p.Ile10Thr | missense_variant | 2/3 | ENST00000296506.8 | |
SCRG1 | NM_001329597.2 | c.29T>C | p.Ile10Thr | missense_variant | 3/4 | ||
SCRG1 | XM_047449563.1 | c.29T>C | p.Ile10Thr | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCRG1 | ENST00000296506.8 | c.29T>C | p.Ile10Thr | missense_variant | 2/3 | 1 | NM_007281.4 | P1 | |
SCRG1 | ENST00000512188.1 | c.29T>C | p.Ile10Thr | missense_variant, NMD_transcript_variant | 7/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000151 AC: 38AN: 251388Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135854
GnomAD4 exome AF: 0.000128 AC: 187AN: 1461864Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 727234
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.29T>C (p.I10T) alteration is located in exon 2 (coding exon 1) of the SCRG1 gene. This alteration results from a T to C substitution at nucleotide position 29, causing the isoleucine (I) at amino acid position 10 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