chr17-74748948-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004252.5(NHERF1):āc.102G>Cā(p.Lys34Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,605,854 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 (ā ).
Frequency
Consequence
NM_004252.5 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 |
---|---|---|---|---|---|---|---|
NHERF1 | NM_004252.5 | c.102G>C | p.Lys34Asn | missense_variant | 1/6 | ENST00000262613.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHERF1 | ENST00000262613.10 | c.102G>C | p.Lys34Asn | missense_variant | 1/6 | 1 | NM_004252.5 | P1 | |
NHERF1 | ENST00000583369.5 | c.102G>C | p.Lys34Asn | missense_variant | 1/3 | 3 | |||
SLC9A3R1-AS1 | ENST00000585285.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000392 AC: 9AN: 229818Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126476
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1453654Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 8AN XY: 723006
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 25, 2023 | This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 34 of the SLC9A3R1 protein (p.Lys34Asn). This variant is present in population databases (rs780010556, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with SLC9A3R1-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at