chr1-39955401-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032793.5(MFSD2A):c.93+16C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,510,868 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0016 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 19 hom. )
Consequence
MFSD2A
NM_032793.5 intron
NM_032793.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0700
Genes affected
MFSD2A (HGNC:25897): (MFSD2 lysolipid transporter A, lysophospholipid) The protein encoded by this gene is a transmembrane protein and sodium-dependent lysophosphatidylcholine transporter. The encoded protein is involved in the establishment of the blood-brain barrier and is required for brain growth and function. Defects in this gene are a cause of a progressive microcephaly syndrome. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 1-39955401-C-A is Benign according to our data. Variant chr1-39955401-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1598360.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00162 (246/152280) while in subpopulation EAS AF= 0.0157 (81/5160). AF 95% confidence interval is 0.0129. There are 1 homozygotes in gnomad4. There are 137 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFSD2A | NM_032793.5 | c.93+16C>A | intron_variant | ENST00000372811.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD2A | ENST00000372811.10 | c.93+16C>A | intron_variant | 1 | NM_032793.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00161 AC: 245AN: 152162Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00467 AC: 631AN: 135100Hom.: 5 AF XY: 0.00363 AC XY: 265AN XY: 73062
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GnomAD4 exome AF: 0.00122 AC: 1664AN: 1358588Hom.: 19 Cov.: 30 AF XY: 0.00117 AC XY: 781AN XY: 667010
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GnomAD4 genome ? AF: 0.00162 AC: 246AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.00184 AC XY: 137AN XY: 74436
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Microcephaly 15, primary, autosomal recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 21, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
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Name
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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