16-2036421-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001130012.3(NHERF2):c.512G>C(p.Arg171Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,126 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R171W) has been classified as Likely benign.
Frequency
Consequence
NM_001130012.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHERF2 | NM_001130012.3 | c.512G>C | p.Arg171Pro | missense_variant | 3/7 | ENST00000424542.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHERF2 | ENST00000424542.7 | c.512G>C | p.Arg171Pro | missense_variant | 3/7 | 1 | NM_001130012.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000425 AC: 1AN: 235410Hom.: 0 AF XY: 0.00000777 AC XY: 1AN XY: 128702
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455126Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 723446
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.512G>C (p.R171P) alteration is located in exon 3 (coding exon 3) of the SLC9A3R2 gene. This alteration results from a G to C substitution at nucleotide position 512, causing the arginine (R) at amino acid position 171 to be replaced by a proline (P). 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