3-57666179-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152678.3(DENND6A):c.376G>T(p.Val126Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152678.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DENND6A | ENST00000311128.10 | c.376G>T | p.Val126Leu | missense_variant | 4/20 | 1 | NM_152678.3 | ENSP00000311401.5 | ||
DENND6A | ENST00000464875.1 | n.202G>T | non_coding_transcript_exon_variant | 4/4 | 2 | |||||
DENND6A | ENST00000487662.1 | n.16G>T | non_coding_transcript_exon_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251336Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135860
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461692Hom.: 0 Cov.: 30 AF XY: 0.0000371 AC XY: 27AN XY: 727154
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.376G>T (p.V126L) alteration is located in exon 4 (coding exon 4) of the DENND6A gene. This alteration results from a G to T substitution at nucleotide position 376, causing the valine (V) at amino acid position 126 to be replaced by a leucine (L). 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