15-72208751-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002654.6(PKM):c.706G>A(p.Asp236Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,614,182 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002654.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251494Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135920
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461892Hom.: 1 Cov.: 32 AF XY: 0.0000839 AC XY: 61AN XY: 727248
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152290Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2021 | The c.706G>A (p.D236N) alteration is located in exon 6 (coding exon 5) of the PKM gene. This alteration results from a G to A substitution at nucleotide position 706, causing the aspartic acid (D) at amino acid position 236 to be replaced by an asparagine (N). 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