17-74748976-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004252.5(NHERF1):c.130C>G(p.Pro44Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,607,066 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P44P) has been classified as Benign.
Frequency
Consequence
NM_004252.5 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 |
---|---|---|---|---|---|---|---|
NHERF1 | NM_004252.5 | c.130C>G | p.Pro44Ala | missense_variant | 1/6 | ENST00000262613.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHERF1 | ENST00000262613.10 | c.130C>G | p.Pro44Ala | missense_variant | 1/6 | 1 | NM_004252.5 | P1 | |
NHERF1 | ENST00000583369.5 | c.130C>G | p.Pro44Ala | missense_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000776 AC: 118AN: 152108Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000262 AC: 60AN: 228628Hom.: 1 AF XY: 0.000215 AC XY: 27AN XY: 125682
GnomAD4 exome AF: 0.0000845 AC: 123AN: 1454840Hom.: 1 Cov.: 32 AF XY: 0.0000788 AC XY: 57AN XY: 723440
GnomAD4 genome ? AF: 0.000775 AC: 118AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.000699 AC XY: 52AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at