rs4129081
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017694.4(MFSD6):c.1532+5121G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,850 control chromosomes in the GnomAD database, including 9,175 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.33 ( 9175 hom., cov: 31)
Exomes 𝑓: 0.20 ( 0 hom. )
Consequence
MFSD6
NM_017694.4 intron
NM_017694.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.106
Genes affected
MFSD6 (HGNC:24711): (major facilitator superfamily domain containing 6) Predicted to enable MHC class I protein binding activity and MHC class I receptor activity. Predicted to be involved in antigen processing and presentation of exogenous peptide antigen via MHC class I. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFSD6 | NM_017694.4 | c.1532+5121G>T | intron_variant | ENST00000392328.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD6 | ENST00000392328.6 | c.1532+5121G>T | intron_variant | 2 | NM_017694.4 | P1 | |||
MFSD6 | ENST00000281416.11 | c.1532+5121G>T | intron_variant | 1 | P1 | ||||
MFSD6 | ENST00000434582.5 | c.138+5121G>T | intron_variant | 5 | |||||
MFSD6 | ENST00000489793.1 | n.107G>T | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.332 AC: 50427AN: 151722Hom.: 9148 Cov.: 31
GnomAD3 genomes
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31
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GnomAD4 exome AF: 0.200 AC: 2AN: 10Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1AN XY: 6
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GnomAD4 genome ? AF: 0.333 AC: 50498AN: 151840Hom.: 9175 Cov.: 31 AF XY: 0.343 AC XY: 25466AN XY: 74198
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at