chr2-190436190-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_017694.4(MFSD6):āc.161T>Cā(p.Ile54Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,614,162 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_017694.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFSD6 | NM_017694.4 | c.161T>C | p.Ile54Thr | missense_variant | 3/8 | ENST00000392328.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD6 | ENST00000392328.6 | c.161T>C | p.Ile54Thr | missense_variant | 3/8 | 2 | NM_017694.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00698 AC: 1062AN: 152226Hom.: 24 Cov.: 33
GnomAD3 exomes AF: 0.00177 AC: 444AN: 251346Hom.: 10 AF XY: 0.00131 AC XY: 178AN XY: 135836
GnomAD4 exome AF: 0.000705 AC: 1031AN: 1461818Hom.: 15 Cov.: 30 AF XY: 0.000562 AC XY: 409AN XY: 727226
GnomAD4 genome AF: 0.00698 AC: 1064AN: 152344Hom.: 24 Cov.: 33 AF XY: 0.00675 AC XY: 503AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at