rs187194973
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_022114.4(PRDM16):c.100G>A(p.Ala34Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00288 in 1,612,890 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A34V) has been classified as Uncertain significance.
Frequency
Consequence
NM_022114.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00185 AC: 281AN: 152224Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00178 AC: 440AN: 247300Hom.: 1 AF XY: 0.00178 AC XY: 240AN XY: 134862
GnomAD4 exome AF: 0.00299 AC: 4368AN: 1460548Hom.: 11 Cov.: 31 AF XY: 0.00292 AC XY: 2120AN XY: 726572
GnomAD4 genome AF: 0.00184 AC: 281AN: 152342Hom.: 1 Cov.: 33 AF XY: 0.00181 AC XY: 135AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:5
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p.Ala34Thr in exon 2 of PRDM16: This variant is not expected to have clinical s ignificance because it has been identified in 0.3% (371/125336) of European chro mosomes by the Genome Aggregation Database Sequencing Project (http://gnomad.bro adinstitute.org; dbSNP rs187194973). ACMG/AMP Criteria applied: BA1 (Richards 20 15). -
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not provided Benign:5
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PRDM16: BP4, BS1, BS2 -
Left ventricular noncompaction 8 Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at