15-23566192-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005664.4(MKRN3):c.410C>T(p.Ala137Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005664.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MKRN3 | NM_005664.4 | c.410C>T | p.Ala137Val | missense_variant | 1/1 | ENST00000314520.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MKRN3 | ENST00000314520.6 | c.410C>T | p.Ala137Val | missense_variant | 1/1 | NM_005664.4 | P1 | ||
ENST00000563044.2 | n.1638G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250222Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135616
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461398Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726996
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74498
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.410C>T (p.A137V) alteration is located in exon 1 (coding exon 1) of the MKRN3 gene. This alteration results from a C to T substitution at nucleotide position 410, causing the alanine (A) at amino acid position 137 to be replaced by a valine (V). 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