NM_001077199.3:c.49C>T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001077199.3(SREK1):c.49C>T(p.Pro17Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,551,682 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001077199.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000454 AC: 7AN: 154220Hom.: 0 AF XY: 0.0000612 AC XY: 5AN XY: 81660
GnomAD4 exome AF: 0.0000121 AC: 17AN: 1399300Hom.: 0 Cov.: 30 AF XY: 0.0000101 AC XY: 7AN XY: 690200
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152382Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74526
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.49C>T (p.P17S) alteration is located in exon 1 (coding exon 1) of the SREK1 gene. This alteration results from a C to T substitution at nucleotide position 49, causing the proline (P) at amino acid position 17 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