chr1-197511754-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001195215.2(DENND1B):āc.1789A>Gā(p.Met597Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00081 in 1,608,678 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001195215.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DENND1B | NM_001195215.2 | c.1789A>G | p.Met597Val | missense_variant | 22/23 | ENST00000620048.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DENND1B | ENST00000620048.6 | c.1789A>G | p.Met597Val | missense_variant | 22/23 | 5 | NM_001195215.2 | P2 | |
DENND1B | ENST00000294737.11 | c.*477A>G | 3_prime_UTR_variant, NMD_transcript_variant | 19/20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00138 AC: 210AN: 151756Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00250 AC: 619AN: 247750Hom.: 8 AF XY: 0.00226 AC XY: 303AN XY: 133924
GnomAD4 exome AF: 0.000751 AC: 1094AN: 1456804Hom.: 11 Cov.: 30 AF XY: 0.000709 AC XY: 514AN XY: 724622
GnomAD4 genome AF: 0.00138 AC: 209AN: 151874Hom.: 0 Cov.: 32 AF XY: 0.00152 AC XY: 113AN XY: 74232
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at