17-74748895-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004252.5(NHERF1):āc.49C>Gā(p.Leu17Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 1,598,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHERF1 | ENST00000262613.10 | c.49C>G | p.Leu17Val | missense_variant | Exon 1 of 6 | 1 | NM_004252.5 | ENSP00000262613.5 | ||
NHERF1 | ENST00000583369.5 | c.49C>G | p.Leu17Val | missense_variant | Exon 1 of 3 | 3 | ENSP00000464321.1 | |||
SLC9A3R1-AS1 | ENST00000585285.1 | n.18G>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000887 AC: 2AN: 225506Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 124976
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1446690Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 719282
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74320
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.49C>G (p.L17V) alteration is located in exon 1 (coding exon 1) of the SLC9A3R1 gene. This alteration results from a C to G substitution at nucleotide position 49, causing the leucine (L) at amino acid position 17 to be replaced by a valine (V). 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