rs10491212
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020772.3(NUFIP2):c.2003-1658G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,056 control chromosomes in the GnomAD database, including 4,261 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 ( 4261 hom., cov: 32)
Consequence
NUFIP2
NM_020772.3 intron
NM_020772.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.206
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUFIP2 | NM_020772.3 | c.2003-1658G>A | intron_variant | ENST00000225388.9 | |||
NUFIP2 | XM_017024896.3 | c.1526-1658G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUFIP2 | ENST00000225388.9 | c.2003-1658G>A | intron_variant | 1 | NM_020772.3 | P1 | |||
NUFIP2 | ENST00000579665.1 | c.278-1658G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.224 AC: 33989AN: 151936Hom.: 4253 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.224 AC: 34039AN: 152056Hom.: 4261 Cov.: 32 AF XY: 0.227 AC XY: 16843AN XY: 74318
GnomAD4 genome
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1256
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3470
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at