chr16-2036483-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001130012.3(NHERF2):c.574G>A(p.Ala192Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,594,726 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHERF2 | NM_001130012.3 | c.574G>A | p.Ala192Thr | missense_variant | 3/7 | ENST00000424542.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHERF2 | ENST00000424542.7 | c.574G>A | p.Ala192Thr | missense_variant | 3/7 | 1 | NM_001130012.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000237 AC: 50AN: 211344Hom.: 0 AF XY: 0.000259 AC XY: 30AN XY: 115708
GnomAD4 exome AF: 0.000205 AC: 296AN: 1442412Hom.: 0 Cov.: 31 AF XY: 0.000211 AC XY: 151AN XY: 716040
GnomAD4 genome AF: 0.000269 AC: 41AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 16, 2021 | The c.574G>A (p.A192T) 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 574, causing the alanine (A) at amino acid position 192 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