rs7581836
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000455668.1(NECAP1P2):n.202T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 161,958 control chromosomes in the GnomAD database, including 2,219 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 0.14 ( 2005 hom., cov: 33)
Exomes 𝑓: 0.16 ( 214 hom. )
Consequence
NECAP1P2
ENST00000455668.1 non_coding_transcript_exon
ENST00000455668.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.287
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=-0.6).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECAP1P2 | ENST00000455668.1 | n.202T>G | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 21975AN: 152124Hom.: 2006 Cov.: 33
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GnomAD4 exome AF: 0.156 AC: 1518AN: 9716Hom.: 214 Cov.: 0 AF XY: 0.152 AC XY: 845AN XY: 5556
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GnomAD4 genome ? AF: 0.144 AC: 21980AN: 152242Hom.: 2005 Cov.: 33 AF XY: 0.147 AC XY: 10970AN XY: 74438
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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