4-173388351-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007281.4(SCRG1):āc.287A>Gā(p.Asn96Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000714 in 1,611,722 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCRG1 | NM_007281.4 | c.287A>G | p.Asn96Ser | missense_variant | 3/3 | ENST00000296506.8 | |
SCRG1 | NM_001329597.2 | c.287A>G | p.Asn96Ser | missense_variant | 4/4 | ||
SCRG1 | XM_047449563.1 | c.287A>G | p.Asn96Ser | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCRG1 | ENST00000296506.8 | c.287A>G | p.Asn96Ser | missense_variant | 3/3 | 1 | NM_007281.4 | P1 | |
SCRG1 | ENST00000512188.1 | c.*306A>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000841 AC: 21AN: 249744Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135054
GnomAD4 exome AF: 0.0000719 AC: 105AN: 1459508Hom.: 0 Cov.: 28 AF XY: 0.0000689 AC XY: 50AN XY: 726118
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.287A>G (p.N96S) alteration is located in exon 3 (coding exon 2) of the SCRG1 gene. This alteration results from a A to G substitution at nucleotide position 287, causing the asparagine (N) at amino acid position 96 to be replaced by a serine (S). 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