chr11-20678030-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006157.5(NELL1):c.154C>T(p.His52Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000248 in 1,614,022 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H52Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_006157.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NELL1 | NM_006157.5 | c.154C>T | p.His52Tyr | missense_variant | 2/20 | ENST00000357134.10 | |
NELL1 | NM_001288713.1 | c.238C>T | p.His80Tyr | missense_variant | 3/21 | ||
NELL1 | NM_201551.2 | c.154C>T | p.His52Tyr | missense_variant | 2/19 | ||
NELL1 | NM_001288714.1 | c.154C>T | p.His52Tyr | missense_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NELL1 | ENST00000357134.10 | c.154C>T | p.His52Tyr | missense_variant | 2/20 | 1 | NM_006157.5 | P1 | |
NELL1 | ENST00000532434.5 | c.154C>T | p.His52Tyr | missense_variant | 2/19 | 1 | |||
NELL1 | ENST00000298925.9 | c.238C>T | p.His80Tyr | missense_variant | 3/21 | 2 | |||
NELL1 | ENST00000325319.9 | c.154C>T | p.His52Tyr | missense_variant | 2/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000350 AC: 88AN: 251394Hom.: 0 AF XY: 0.000375 AC XY: 51AN XY: 135864
GnomAD4 exome AF: 0.000254 AC: 372AN: 1461814Hom.: 0 Cov.: 32 AF XY: 0.000261 AC XY: 190AN XY: 727212
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.154C>T (p.H52Y) alteration is located in exon 2 (coding exon 2) of the NELL1 gene. This alteration results from a C to T substitution at nucleotide position 154, causing the histidine (H) at amino acid position 52 to be replaced by a tyrosine (Y). 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