9-35793894-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_003995.4(NPR2):c.668-4C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000681 in 1,614,140 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003995.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPR2 | NM_003995.4 | c.668-4C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000342694.7 | |||
NPR2 | NM_001378923.1 | c.668-4C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPR2 | ENST00000342694.7 | c.668-4C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003995.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00348 AC: 530AN: 152152Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000847 AC: 213AN: 251476Hom.: 0 AF XY: 0.000640 AC XY: 87AN XY: 135908
GnomAD4 exome AF: 0.000389 AC: 569AN: 1461870Hom.: 7 Cov.: 31 AF XY: 0.000344 AC XY: 250AN XY: 727242
GnomAD4 genome AF: 0.00349 AC: 531AN: 152270Hom.: 5 Cov.: 32 AF XY: 0.00333 AC XY: 248AN XY: 74448
ClinVar
Submissions by phenotype
Acromesomelic dysplasia 1, Maroteaux type;C4014690:Tall stature-scoliosis-macrodactyly of the great toes syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at