chr13-101229426-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_052867.4(NALCN):c.1593C>T(p.Val531=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,602,124 control chromosomes in the GnomAD database, including 95,758 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. V531V) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NALCN | NM_052867.4 | c.1593C>T | p.Val531= | synonymous_variant | 13/44 | ENST00000251127.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NALCN | ENST00000251127.11 | c.1593C>T | p.Val531= | synonymous_variant | 13/44 | 1 | NM_052867.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.271 AC: 41121AN: 151930Hom.: 6584 Cov.: 33
GnomAD3 exomes AF: 0.283 AC: 68633AN: 242156Hom.: 11302 AF XY: 0.293 AC XY: 38389AN XY: 131080
GnomAD4 exome AF: 0.341 AC: 494986AN: 1450078Hom.: 89173 Cov.: 34 AF XY: 0.342 AC XY: 246460AN XY: 721260
GnomAD4 genome AF: 0.270 AC: 41118AN: 152046Hom.: 6585 Cov.: 33 AF XY: 0.269 AC XY: 19973AN XY: 74312
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Hypotonia, infantile, with psychomotor retardation and characteristic facies 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Congenital contractures of the limbs and face, hypotonia, and developmental delay Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at