1-153941294-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014856.3(DENND4B):c.1123-5T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 1,613,414 control chromosomes in the GnomAD database, including 231,295 homozygotes. 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.
Frequency
Consequence
NM_014856.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DENND4B | ENST00000361217.9 | c.1123-5T>C | splice_region_variant, intron_variant | Intron 7 of 27 | 1 | NM_014856.3 | ENSP00000354597.4 | |||
DENND4B | ENST00000368646.6 | c.1156-5T>C | splice_region_variant, intron_variant | Intron 7 of 21 | 5 | ENSP00000357635.2 | ||||
DENND4B | ENST00000483561.2 | n.444-5T>C | splice_region_variant, intron_variant | Intron 2 of 2 | 4 | |||||
DENND4B | ENST00000494683.1 | n.62-5T>C | splice_region_variant, intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.584 AC: 88720AN: 151842Hom.: 27120 Cov.: 31
GnomAD3 exomes AF: 0.585 AC: 145571AN: 248696Hom.: 45059 AF XY: 0.578 AC XY: 78009AN XY: 134938
GnomAD4 exome AF: 0.519 AC: 758304AN: 1461454Hom.: 204128 Cov.: 63 AF XY: 0.520 AC XY: 378105AN XY: 726994
GnomAD4 genome AF: 0.585 AC: 88823AN: 151960Hom.: 27167 Cov.: 31 AF XY: 0.594 AC XY: 44107AN XY: 74282
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at