1-3411986-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_022114.4(PRDM16):c.1789G>C(p.Asp597His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,364 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D597N) has been classified as Uncertain significance.
Frequency
Consequence
NM_022114.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249080Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135240
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461364Hom.: 0 Cov.: 37 AF XY: 0.00000275 AC XY: 2AN XY: 726994
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1789G>C (p.D597H) alteration is located in exon 9 (coding exon 9) of the PRDM16 gene. This alteration results from a G to C substitution at nucleotide position 1789, causing the aspartic acid (D) at amino acid position 597 to be replaced by a histidine (H). 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