chr2-190436227-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_017694.4(MFSD6):c.198C>T(p.Asn66=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,614,020 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0033 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00088 ( 12 hom. )
Consequence
MFSD6
NM_017694.4 synonymous
NM_017694.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.02
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 2-190436227-C-T is Benign according to our data. Variant chr2-190436227-C-T is described in ClinVar as [Benign]. Clinvar id is 772854.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.02 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFSD6 | NM_017694.4 | c.198C>T | p.Asn66= | synonymous_variant | 3/8 | ENST00000392328.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD6 | ENST00000392328.6 | c.198C>T | p.Asn66= | synonymous_variant | 3/8 | 2 | NM_017694.4 | P1 | |
MFSD6 | ENST00000281416.11 | c.198C>T | p.Asn66= | synonymous_variant | 1/6 | 1 | P1 | ||
MFSD6 | ENST00000445546.1 | c.198C>T | p.Asn66= | synonymous_variant | 2/2 | 4 | |||
MFSD6 | ENST00000432036.5 | c.198C>T | p.Asn66= | synonymous_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00328 AC: 499AN: 152200Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00139 AC: 350AN: 251098Hom.: 0 AF XY: 0.00118 AC XY: 160AN XY: 135712
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GnomAD4 exome AF: 0.000877 AC: 1282AN: 1461702Hom.: 12 Cov.: 30 AF XY: 0.000890 AC XY: 647AN XY: 727182
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GnomAD4 genome AF: 0.00328 AC: 499AN: 152318Hom.: 1 Cov.: 33 AF XY: 0.00310 AC XY: 231AN XY: 74482
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2017 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at