17-62736189-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_152598.4(MARCHF10):c.1679C>T(p.Thr560Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00804 in 1,614,200 control chromosomes in the GnomAD database, including 77 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 Benign (no stars).
Frequency
Consequence
NM_152598.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MARCHF10 | NM_152598.4 | c.1679C>T | p.Thr560Ile | missense_variant | Exon 6 of 11 | ENST00000311269.10 | NP_689811.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00733 AC: 1116AN: 152204Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00717 AC: 1800AN: 251016Hom.: 16 AF XY: 0.00752 AC XY: 1020AN XY: 135670
GnomAD4 exome AF: 0.00811 AC: 11856AN: 1461878Hom.: 71 Cov.: 32 AF XY: 0.00807 AC XY: 5872AN XY: 727234
GnomAD4 genome AF: 0.00732 AC: 1115AN: 152322Hom.: 6 Cov.: 32 AF XY: 0.00737 AC XY: 549AN XY: 74478
ClinVar
Submissions by phenotype
MARCHF10-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at