17-74748978-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_004252.5(NHERF1):c.132C>T(p.Pro44Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000522 in 1,607,122 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004252.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHERF1 | ENST00000262613.10 | c.132C>T | p.Pro44Pro | synonymous_variant | Exon 1 of 6 | 1 | NM_004252.5 | ENSP00000262613.5 | ||
NHERF1 | ENST00000583369.5 | c.132C>T | p.Pro44Pro | synonymous_variant | Exon 1 of 3 | 3 | ENSP00000464321.1 |
Frequencies
GnomAD3 genomes AF: 0.00285 AC: 434AN: 152160Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000652 AC: 149AN: 228552Hom.: 4 AF XY: 0.000430 AC XY: 54AN XY: 125690
GnomAD4 exome AF: 0.000279 AC: 406AN: 1454844Hom.: 3 Cov.: 32 AF XY: 0.000220 AC XY: 159AN XY: 723452
GnomAD4 genome AF: 0.00284 AC: 433AN: 152278Hom.: 3 Cov.: 33 AF XY: 0.00267 AC XY: 199AN XY: 74464
ClinVar
Submissions by phenotype
NHERF1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at