chr2-190436516-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_017694.4(MFSD6):āc.487A>Gā(p.Ile163Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,614,114 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 (ā ).
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.487A>G | p.Ile163Val | missense_variant | 3/8 | ENST00000392328.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD6 | ENST00000392328.6 | c.487A>G | p.Ile163Val | missense_variant | 3/8 | 2 | NM_017694.4 | P1 | |
MFSD6 | ENST00000281416.11 | c.487A>G | p.Ile163Val | missense_variant | 1/6 | 1 | P1 | ||
MFSD6 | ENST00000445546.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251464Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135908
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461880Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 727238
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.487A>G (p.I163V) alteration is located in exon 3 (coding exon 1) of the MFSD6 gene. This alteration results from a A to G substitution at nucleotide position 487, causing the isoleucine (I) at amino acid position 163 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