17-7316233-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_032442.3(NEURL4):c.4579G>A(p.Ala1527Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000656 in 1,613,772 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032442.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEURL4 | ENST00000399464.7 | c.4579G>A | p.Ala1527Thr | missense_variant | Exon 29 of 29 | 1 | NM_032442.3 | ENSP00000382390.2 | ||
ENSG00000261915 | ENST00000575474.1 | n.975+43G>A | intron_variant | Intron 8 of 18 | 5 | ENSP00000468772.1 |
Frequencies
GnomAD3 genomes AF: 0.000914 AC: 139AN: 152138Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00114 AC: 284AN: 249484Hom.: 2 AF XY: 0.00116 AC XY: 157AN XY: 135374
GnomAD4 exome AF: 0.000629 AC: 919AN: 1461516Hom.: 3 Cov.: 31 AF XY: 0.000612 AC XY: 445AN XY: 727050
GnomAD4 genome AF: 0.000913 AC: 139AN: 152256Hom.: 1 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
NEURL4: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at