chr2-205716309-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003872.3(NRP2):c.368A>G(p.Lys123Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00639 in 1,614,066 control chromosomes in the GnomAD database, including 608 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003872.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRP2 | NM_003872.3 | c.368A>G | p.Lys123Arg | missense_variant | 3/17 | ENST00000357785.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRP2 | ENST00000357785.10 | c.368A>G | p.Lys123Arg | missense_variant | 3/17 | 1 | NM_003872.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0323 AC: 4915AN: 152058Hom.: 291 Cov.: 31
GnomAD4 exome AF: 0.00369 AC: 5390AN: 1461890Hom.: 317 Cov.: 31 AF XY: 0.00327 AC XY: 2377AN XY: 727246
GnomAD4 genome ? AF: 0.0323 AC: 4920AN: 152176Hom.: 291 Cov.: 31 AF XY: 0.0313 AC XY: 2329AN XY: 74400
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at