12-50674556-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP2BP4_ModerateBS2
The NM_173602.3(DIP2B):c.723C>A(p.Asp241Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173602.3 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIP2B | NM_173602.3 | c.723C>A | p.Asp241Glu | missense_variant | 6/38 | ENST00000301180.10 | NP_775873.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIP2B | ENST00000301180.10 | c.723C>A | p.Asp241Glu | missense_variant | 6/38 | 5 | NM_173602.3 | ENSP00000301180.5 | ||
DIP2B | ENST00000546719.1 | n.500C>A | non_coding_transcript_exon_variant | 5/7 | 1 | |||||
DIP2B | ENST00000549620.5 | n.879C>A | non_coding_transcript_exon_variant | 6/8 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251390Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135870
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461880Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2023 | The c.723C>A (p.D241E) alteration is located in exon 6 (coding exon 6) of the DIP2B gene. This alteration results from a C to A substitution at nucleotide position 723, causing the aspartic acid (D) at amino acid position 241 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at