NM_032793.5:c.-246C>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032793.5(MFSD2A):c.-246C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 370,050 control chromosomes in the GnomAD database, including 3,997 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.079 ( 1134 hom., cov: 31)
Exomes 𝑓: 0.068 ( 2863 hom. )
Consequence
MFSD2A
NM_032793.5 upstream_gene
NM_032793.5 upstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.132
Publications
3 publications found
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]
MFSD2A Gene-Disease associations (from GenCC):
- microcephaly 15, primary, autosomal recessiveInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- autosomal recessive primary microcephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 1-39955047-C-A is Benign according to our data. Variant chr1-39955047-C-A is described in ClinVar as Benign. ClinVar VariationId is 1223952.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0790 AC: 11942AN: 151172Hom.: 1128 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
11942
AN:
151172
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0681 AC: 14891AN: 218760Hom.: 2863 AF XY: 0.0649 AC XY: 7193AN XY: 110810 show subpopulations
GnomAD4 exome
AF:
AC:
14891
AN:
218760
Hom.:
AF XY:
AC XY:
7193
AN XY:
110810
show subpopulations
African (AFR)
AF:
AC:
1049
AN:
6484
American (AMR)
AF:
AC:
839
AN:
6362
Ashkenazi Jewish (ASJ)
AF:
AC:
96
AN:
8428
East Asian (EAS)
AF:
AC:
10297
AN:
20654
South Asian (SAS)
AF:
AC:
150
AN:
2152
European-Finnish (FIN)
AF:
AC:
712
AN:
18298
Middle Eastern (MID)
AF:
AC:
22
AN:
1164
European-Non Finnish (NFE)
AF:
AC:
731
AN:
140554
Other (OTH)
AF:
AC:
995
AN:
14664
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
426
852
1279
1705
2131
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
82
164
246
328
410
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0791 AC: 11968AN: 151290Hom.: 1134 Cov.: 31 AF XY: 0.0833 AC XY: 6154AN XY: 73880 show subpopulations
GnomAD4 genome
AF:
AC:
11968
AN:
151290
Hom.:
Cov.:
31
AF XY:
AC XY:
6154
AN XY:
73880
show subpopulations
African (AFR)
AF:
AC:
6601
AN:
41182
American (AMR)
AF:
AC:
1850
AN:
15210
Ashkenazi Jewish (ASJ)
AF:
AC:
41
AN:
3462
East Asian (EAS)
AF:
AC:
2221
AN:
5018
South Asian (SAS)
AF:
AC:
352
AN:
4754
European-Finnish (FIN)
AF:
AC:
411
AN:
10528
Middle Eastern (MID)
AF:
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
AC:
331
AN:
67840
Other (OTH)
AF:
AC:
157
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
464
928
1393
1857
2321
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
124
248
372
496
620
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
944
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
May 15, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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