1-3426240-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022114.4(PRDM16):c.3284+15G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,607,588 control chromosomes in the GnomAD database, including 70,065 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_022114.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.320 AC: 48586AN: 151736Hom.: 8215 Cov.: 31
GnomAD3 exomes AF: 0.295 AC: 72759AN: 246792Hom.: 11317 AF XY: 0.291 AC XY: 38968AN XY: 133982
GnomAD4 exome AF: 0.288 AC: 419424AN: 1455734Hom.: 61834 Cov.: 31 AF XY: 0.287 AC XY: 207530AN XY: 723644
GnomAD4 genome AF: 0.320 AC: 48655AN: 151854Hom.: 8231 Cov.: 31 AF XY: 0.317 AC XY: 23505AN XY: 74194
ClinVar
Submissions by phenotype
not specified Benign:6
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3284+15G>T in intron 14 of PRDM16: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus se quence. It has been identified in 40.6% (1578/3884) of African American chromoso mes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs .washington.edu/EVS; dbSNP rs870171). -
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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Left ventricular noncompaction 8 Benign:2
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at