chr1-3417929-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_022114.4(PRDM16):c.2793C>T(p.Asn931Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0027 in 1,516,430 control chromosomes in the GnomAD database, including 92 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_022114.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0139 AC: 2091AN: 149958Hom.: 48 Cov.: 33
GnomAD3 exomes AF: 0.00335 AC: 829AN: 247292Hom.: 15 AF XY: 0.00245 AC XY: 329AN XY: 134408
GnomAD4 exome AF: 0.00147 AC: 2002AN: 1366354Hom.: 44 Cov.: 35 AF XY: 0.00125 AC XY: 851AN XY: 681432
GnomAD4 genome AF: 0.0139 AC: 2090AN: 150076Hom.: 48 Cov.: 33 AF XY: 0.0136 AC XY: 997AN XY: 73404
ClinVar
Submissions by phenotype
not specified Benign:6
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Asn931Asn in exon 11 of PRDM16: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 4.5% (172/3804) of African American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (http://evs.gs.washington.edu/EVS; dbSNP rs59135929). -
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not provided 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). -
Left ventricular noncompaction 8 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at