chr16-2036480-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001130012.3(NHERF2):c.571C>G(p.Arg191Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000818 in 1,596,964 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130012.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHERF2 | NM_001130012.3 | c.571C>G | p.Arg191Gly | missense_variant | 3/7 | ENST00000424542.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHERF2 | ENST00000424542.7 | c.571C>G | p.Arg191Gly | missense_variant | 3/7 | 1 | NM_001130012.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000558 AC: 85AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000506 AC: 109AN: 215234Hom.: 0 AF XY: 0.000365 AC XY: 43AN XY: 117796
GnomAD4 exome AF: 0.000845 AC: 1221AN: 1444622Hom.: 1 Cov.: 32 AF XY: 0.000778 AC XY: 558AN XY: 717338
GnomAD4 genome ? AF: 0.000558 AC: 85AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000591 AC XY: 44AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.571C>G (p.R191G) alteration is located in exon 3 (coding exon 3) of the SLC9A3R2 gene. This alteration results from a C to G substitution at nucleotide position 571, causing the arginine (R) at amino acid position 191 to be replaced by a glycine (G). 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