2-205697593-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_003872.3(NRP2):c.123C>T(p.Thr41Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00384 in 1,613,984 control chromosomes in the GnomAD database, including 204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003872.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0201 AC: 3060AN: 152006Hom.: 101 Cov.: 31
GnomAD3 exomes AF: 0.00541 AC: 1359AN: 251184Hom.: 48 AF XY: 0.00398 AC XY: 541AN XY: 135826
GnomAD4 exome AF: 0.00215 AC: 3138AN: 1461860Hom.: 103 Cov.: 32 AF XY: 0.00187 AC XY: 1358AN XY: 727236
GnomAD4 genome AF: 0.0201 AC: 3065AN: 152124Hom.: 101 Cov.: 31 AF XY: 0.0193 AC XY: 1439AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:2
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NRP2-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