17-62736249-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152598.4(MARCHF10):c.1619C>T(p.Ala540Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,614,070 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_152598.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MARCHF10 | NM_152598.4 | c.1619C>T | p.Ala540Val | missense_variant | Exon 6 of 11 | ENST00000311269.10 | NP_689811.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251172Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135754
GnomAD4 exome AF: 0.000155 AC: 227AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 117AN XY: 727244
GnomAD4 genome AF: 0.000151 AC: 23AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1619C>T (p.A540V) alteration is located in exon 6 (coding exon 5) of the MARCH10 gene. This alteration results from a C to T substitution at nucleotide position 1619, causing the alanine (A) at amino acid position 540 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