chr19-6468091-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024898.4(DENND1C):c.1819G>A(p.Asp607Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,346 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_024898.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151934Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000684 AC: 17AN: 248428Hom.: 0 AF XY: 0.0000668 AC XY: 9AN XY: 134808
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461412Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 726982
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151934Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74188
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1819G>A (p.D607N) alteration is located in exon 23 (coding exon 23) of the DENND1C gene. This alteration results from a G to A substitution at nucleotide position 1819, causing the aspartic acid (D) at amino acid position 607 to be replaced by an asparagine (N). 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