chr13-101055447-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_052867.4(NALCN):c.5065C>T(p.Arg1689Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000164 in 1,614,062 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1689Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_052867.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NALCN | NM_052867.4 | c.5065C>T | p.Arg1689Trp | missense_variant | 44/44 | ENST00000251127.11 | |
NALCN-AS1 | NR_047687.1 | n.770+1G>A | splice_donor_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NALCN | ENST00000251127.11 | c.5065C>T | p.Arg1689Trp | missense_variant | 44/44 | 1 | NM_052867.4 | P1 | |
NALCN-AS1 | ENST00000457843.1 | n.770+1G>A | splice_donor_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000203 AC: 51AN: 251386Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135856
GnomAD4 exome AF: 0.000161 AC: 236AN: 1461834Hom.: 1 Cov.: 31 AF XY: 0.000149 AC XY: 108AN XY: 727220
GnomAD4 genome AF: 0.000184 AC: 28AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74426
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 22, 2020 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at