2-190437204-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_017694.4(MFSD6):c.1175G>A(p.Arg392His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,614,152 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R392C) has been classified as Uncertain significance.
Frequency
Consequence
NM_017694.4 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 |
---|---|---|---|---|---|---|---|
MFSD6 | NM_017694.4 | c.1175G>A | p.Arg392His | missense_variant | 3/8 | ENST00000392328.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD6 | ENST00000392328.6 | c.1175G>A | p.Arg392His | missense_variant | 3/8 | 2 | NM_017694.4 | P1 | |
MFSD6 | ENST00000281416.11 | c.1175G>A | p.Arg392His | missense_variant | 1/6 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251436Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135902
GnomAD4 exome AF: 0.0000711 AC: 104AN: 1461882Hom.: 0 Cov.: 33 AF XY: 0.0000949 AC XY: 69AN XY: 727238
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.1175G>A (p.R392H) alteration is located in exon 3 (coding exon 1) of the MFSD6 gene. This alteration results from a G to A substitution at nucleotide position 1175, causing the arginine (R) at amino acid position 392 to be replaced by a histidine (H). 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