17-4499263-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001124758.3(SPNS2):c.216C>T(p.Pro72Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,474,560 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001124758.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00508 AC: 769AN: 151404Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.000540 AC: 43AN: 79668Hom.: 1 AF XY: 0.000373 AC XY: 17AN XY: 45578
GnomAD4 exome AF: 0.000546 AC: 722AN: 1323048Hom.: 7 Cov.: 32 AF XY: 0.000501 AC XY: 327AN XY: 652112
GnomAD4 genome AF: 0.00508 AC: 770AN: 151512Hom.: 6 Cov.: 32 AF XY: 0.00490 AC XY: 363AN XY: 74024
ClinVar
Submissions by phenotype
SPNS2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at