rs1128723
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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.*1763A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,616 control chromosomes in the GnomAD database, including 2,385 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 0.17 ( 2385 hom., cov: 32)
Exomes 𝑓: 0.083 ( 0 hom. )
Consequence
MFSD6
NM_017694.4 3_prime_UTR
NM_017694.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0540
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=-0.59).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MFSD6 | NM_017694.4 | c.*1763A>G | 3_prime_UTR_variant | 8/8 | ENST00000392328.6 | NP_060164.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MFSD6 | ENST00000392328.6 | c.*1763A>G | 3_prime_UTR_variant | 8/8 | 2 | NM_017694.4 | ENSP00000376141 | P1 | ||
MFSD6 | ENST00000281416.11 | c.*1763A>G | 3_prime_UTR_variant | 6/6 | 1 | ENSP00000281416 | P1 | |||
MFSD6 | ENST00000434582.5 | c.*1956A>G | 3_prime_UTR_variant | 7/7 | 5 | ENSP00000397276 | ||||
MFSD6 | ENST00000412482.1 | c.*58+1705A>G | intron_variant, NMD_transcript_variant | 3 | ENSP00000404511 |
Frequencies
GnomAD3 genomes AF: 0.171 AC: 26045AN: 152068Hom.: 2383 Cov.: 32
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GnomAD4 exome AF: 0.0829 AC: 36AN: 434Hom.: 0 Cov.: 0 AF XY: 0.0802 AC XY: 21AN XY: 262
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GnomAD4 genome AF: 0.171 AC: 26063AN: 152182Hom.: 2385 Cov.: 32 AF XY: 0.167 AC XY: 12459AN XY: 74408
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ClinVar
Not reported inComputational scores
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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