10-69103942-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002727.4(SRGN):c.299C>T(p.Ser100Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000343 in 1,614,124 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002727.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGN | NM_002727.4 | c.299C>T | p.Ser100Phe | missense_variant | 3/3 | ENST00000242465.4 | |
SRGN | NM_001321053.2 | c.299C>T | p.Ser100Phe | missense_variant | 4/4 | ||
SRGN | NM_001321054.1 | c.131C>T | p.Ser44Phe | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGN | ENST00000242465.4 | c.299C>T | p.Ser100Phe | missense_variant | 3/3 | 1 | NM_002727.4 | P1 | |
SRGN | ENST00000462445.1 | n.203C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00207 AC: 315AN: 152158Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000453 AC: 114AN: 251480Hom.: 0 AF XY: 0.000338 AC XY: 46AN XY: 135918
GnomAD4 exome AF: 0.000163 AC: 239AN: 1461848Hom.: 0 Cov.: 30 AF XY: 0.000147 AC XY: 107AN XY: 727230
GnomAD4 genome ? AF: 0.00207 AC: 315AN: 152276Hom.: 1 Cov.: 32 AF XY: 0.00193 AC XY: 144AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at