rs41534051
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_199044.4(NSUN4):c.*1216T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,926 control chromosomes in the GnomAD database, including 4,275 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 4274 hom., cov: 31)
Exomes 𝑓: 0.67 ( 1 hom. )
Consequence
NSUN4
NM_199044.4 3_prime_UTR
NM_199044.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0430
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSUN4 | NM_199044.4 | c.*1216T>C | 3_prime_UTR_variant | 6/6 | ENST00000474844.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSUN4 | ENST00000474844.6 | c.*1216T>C | 3_prime_UTR_variant | 6/6 | 1 | NM_199044.4 | P1 | ||
NSUN4 | ENST00000307089.7 | c.*1760T>C | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.224 AC: 33982AN: 151802Hom.: 4274 Cov.: 31
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31
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GnomAD4 exome AF: 0.667 AC: 4AN: 6Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome ? AF: 0.224 AC: 33977AN: 151920Hom.: 4274 Cov.: 31 AF XY: 0.219 AC XY: 16257AN XY: 74224
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at