chr16-2036420-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001130012.3(NHERF2):c.511C>T(p.Arg171Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,607,594 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R171P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001130012.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHERF2 | NM_001130012.3 | c.511C>T | p.Arg171Trp | missense_variant | 3/7 | ENST00000424542.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHERF2 | ENST00000424542.7 | c.511C>T | p.Arg171Trp | missense_variant | 3/7 | 1 | NM_001130012.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00341 AC: 519AN: 152226Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00339 AC: 800AN: 235794Hom.: 7 AF XY: 0.00343 AC XY: 442AN XY: 128900
GnomAD4 exome AF: 0.00543 AC: 7897AN: 1455250Hom.: 27 Cov.: 32 AF XY: 0.00529 AC XY: 3830AN XY: 723500
GnomAD4 genome ? AF: 0.00341 AC: 519AN: 152344Hom.: 1 Cov.: 33 AF XY: 0.00336 AC XY: 250AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | NHERF2: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at