11-63904823-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_001039469.3(MARK2):c.1714G>A(p.Ala572Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039469.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MARK2 | NM_001039469.3 | c.1714G>A | p.Ala572Thr | missense_variant | 16/19 | ENST00000402010.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MARK2 | ENST00000402010.8 | c.1714G>A | p.Ala572Thr | missense_variant | 16/19 | 1 | NM_001039469.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151916Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251256Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135792
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461836Hom.: 0 Cov.: 35 AF XY: 0.00000963 AC XY: 7AN XY: 727232
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151916Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74162
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.1714G>A (p.A572T) alteration is located in exon 16 (coding exon 16) of the MARK2 gene. This alteration results from a G to A substitution at nucleotide position 1714, causing the alanine (A) at amino acid position 572 to be replaced by a threonine (T). 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