rs1163868389
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004252.5(NHERF1):c.44G>A(p.Cys15Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000138 in 1,446,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004252.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHERF1 | NM_004252.5 | c.44G>A | p.Cys15Tyr | missense_variant | Exon 1 of 6 | ENST00000262613.10 | NP_004243.1 | |
SLC9A3R1-AS1 | NR_187307.1 | n.843C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | ||||
MIR3615 | NR_037409.1 | n.*191G>A | downstream_gene_variant | |||||
MIR3615 | unassigned_transcript_3091 | n.*207G>A | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHERF1 | ENST00000262613.10 | c.44G>A | p.Cys15Tyr | missense_variant | Exon 1 of 6 | 1 | NM_004252.5 | ENSP00000262613.5 | ||
NHERF1 | ENST00000583369.5 | c.44G>A | p.Cys15Tyr | missense_variant | Exon 1 of 3 | 3 | ENSP00000464321.1 | |||
SLC9A3R1-AS1 | ENST00000585285.1 | n.23C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
MIR3615 | ENST00000581999.1 | n.*191G>A | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1446022Hom.: 0 Cov.: 32 AF XY: 0.00000278 AC XY: 2AN XY: 718980
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.