7-100486904-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173564.4(NYAP1):c.152C>T(p.Ser51Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,584,140 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173564.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000208 AC: 4AN: 192214Hom.: 0 AF XY: 0.0000282 AC XY: 3AN XY: 106400
GnomAD4 exome AF: 0.0000342 AC: 49AN: 1432028Hom.: 0 Cov.: 32 AF XY: 0.0000324 AC XY: 23AN XY: 710534
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.152C>T (p.S51L) alteration is located in exon 3 (coding exon 2) of the NYAP1 gene. This alteration results from a C to T substitution at nucleotide position 152, causing the serine (S) at amino acid position 51 to be replaced by a leucine (L). 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