rs2072374
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP7
The NM_014865.4(NCAPD2):c.3300T>A(p.Arg1100=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R1100R) has been classified as Benign.
Frequency
Consequence
NM_014865.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCAPD2 | NM_014865.4 | c.3300T>A | p.Arg1100= | splice_region_variant, synonymous_variant | 26/32 | ENST00000315579.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCAPD2 | ENST00000315579.10 | c.3300T>A | p.Arg1100= | splice_region_variant, synonymous_variant | 26/32 | 1 | NM_014865.4 | P1 | |
NCAPD2 | ENST00000535804.1 | n.133T>A | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
NCAPD2 | ENST00000539084.5 | c.*2995T>A | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 25/31 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1455508Hom.: 0 Cov.: 56 AF XY: 0.00 AC XY: 0AN XY: 722592
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at