NM_001371596.2:c.*2309G>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001371596.2(MFSD8):c.*2309G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000315 in 152,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00032 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
MFSD8
NM_001371596.2 3_prime_UTR
NM_001371596.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.148
Publications
0 publications found
Genes affected
MFSD8 (HGNC:28486): (major facilitator superfamily domain containing 8) This gene encodes a ubiquitous integral membrane protein that contains a transporter domain and a major facilitator superfamily (MFS) domain. Other members of the major facilitator superfamily transport small solutes through chemiosmotic ion gradients. The substrate transported by this protein is unknown. The protein likely localizes to lysosomal membranes. Mutations in this gene are correlated with a variant form of late infantile-onset neuronal ceroid lipofuscinoses (vLINCL). [provided by RefSeq, Oct 2008]
MFSD8 Gene-Disease associations (from GenCC):
- neuronal ceroid lipofuscinosisInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- neuronal ceroid lipofuscinosis 7Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Orphanet
- macular dystrophy with central cone involvementInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001371596.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MFSD8 | NM_001371596.2 | MANE Select | c.*2309G>A | 3_prime_UTR | Exon 12 of 12 | NP_001358525.1 | Q8NHS3-1 | ||
| MFSD8 | NM_001371591.2 | c.*2309G>A | 3_prime_UTR | Exon 12 of 12 | NP_001358520.1 | ||||
| MFSD8 | NM_001371592.2 | c.*2309G>A | 3_prime_UTR | Exon 12 of 12 | NP_001358521.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MFSD8 | ENST00000641686.2 | MANE Select | c.*2309G>A | 3_prime_UTR | Exon 12 of 12 | ENSP00000493218.2 | Q8NHS3-1 | ||
| MFSD8 | ENST00000296468.8 | TSL:1 | c.*2309G>A | 3_prime_UTR | Exon 13 of 13 | ENSP00000296468.3 | Q8NHS3-1 | ||
| MFSD8 | ENST00000503928.2 | TSL:1 | n.211G>A | non_coding_transcript_exon | Exon 3 of 3 |
Frequencies
GnomAD3 genomes 0.000316 AC: 48AN: 152090Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
48
AN:
152090
Hom.:
Cov.:
32
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 Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome 0.000315 AC: 48AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74420 show subpopulations
GnomAD4 genome
AF:
AC:
48
AN:
152208
Hom.:
Cov.:
32
AF XY:
AC XY:
22
AN XY:
74420
show subpopulations
African (AFR)
AF:
AC:
6
AN:
41538
American (AMR)
AF:
AC:
1
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5176
South Asian (SAS)
AF:
AC:
0
AN:
4818
European-Finnish (FIN)
AF:
AC:
0
AN:
10594
Middle Eastern (MID)
AF:
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
AC:
40
AN:
68022
Other (OTH)
AF:
AC:
0
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
3
5
8
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13
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
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8
10
<30
30-35
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Neuronal ceroid lipofuscinosis 7 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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