chr13-101055433-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_052867.4(NALCN):c.5079G>A(p.Arg1693=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R1693R) has been classified as Likely benign.
Frequency
Consequence
NM_052867.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NALCN | NM_052867.4 | c.5079G>A | p.Arg1693= | synonymous_variant | 44/44 | ENST00000251127.11 | |
NALCN-AS1 | NR_047687.1 | n.757C>T | non_coding_transcript_exon_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NALCN | ENST00000251127.11 | c.5079G>A | p.Arg1693= | synonymous_variant | 44/44 | 1 | NM_052867.4 | P1 | |
NALCN-AS1 | ENST00000457843.1 | n.757C>T | non_coding_transcript_exon_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251452Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135892
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727236
GnomAD4 genome AF: 0.000105 AC: 16AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74318
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 26, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at