16-2036465-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000424542.7(NHERF2):c.556G>A(p.Ala186Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,600,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000424542.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHERF2 | NM_001130012.3 | c.556G>A | p.Ala186Thr | missense_variant | 3/7 | ENST00000424542.7 | NP_001123484.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHERF2 | ENST00000424542.7 | c.556G>A | p.Ala186Thr | missense_variant | 3/7 | 1 | NM_001130012.3 | ENSP00000408005 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000121 AC: 27AN: 222724Hom.: 0 AF XY: 0.000148 AC XY: 18AN XY: 121902
GnomAD4 exome AF: 0.000121 AC: 175AN: 1448598Hom.: 0 Cov.: 31 AF XY: 0.000133 AC XY: 96AN XY: 719656
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.556G>A (p.A186T) alteration is located in exon 3 (coding exon 3) of the SLC9A3R2 gene. This alteration results from a G to A substitution at nucleotide position 556, causing the alanine (A) at amino acid position 186 to be replaced by a threonine (T). 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