rs199853370
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_022114.4(PRDM16):c.3102C>T(p.Asn1034Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00207 in 1,613,524 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_022114.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00151 AC: 229AN: 152154Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00181 AC: 451AN: 248886Hom.: 2 AF XY: 0.00203 AC XY: 274AN XY: 135158
GnomAD4 exome AF: 0.00213 AC: 3117AN: 1461252Hom.: 11 Cov.: 32 AF XY: 0.00215 AC XY: 1566AN XY: 726978
GnomAD4 genome AF: 0.00150 AC: 228AN: 152272Hom.: 1 Cov.: 32 AF XY: 0.00145 AC XY: 108AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:6
PRDM16: BP4, BP7 -
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not specified Benign:2
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Left ventricular noncompaction 8 Benign:2
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PRDM16-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at