17-28395020-G-GAA
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_080669.6(SLC46A1):c.*4634_*4635dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
SLC46A1
NM_080669.6 3_prime_UTR
NM_080669.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.395
Publications
3 publications found
Genes affected
SLC46A1 (HGNC:30521): (solute carrier family 46 member 1) This gene encodes a transmembrane proton-coupled folate transporter protein that facilitates the movement of folate and antifolate substrates across cell membranes, optimally in acidic pH environments. This protein is also expressed in the brain and choroid plexus where it transports folates into the central nervous system. This protein further functions as a heme transporter in duodenal enterocytes, and potentially in other tissues like liver and kidney. Its localization to the apical membrane or cytoplasm of intestinal cells is modulated by dietary iron levels. Mutations in this gene are associated with autosomal recessive hereditary folate malabsorption disease. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
SARM1 (HGNC:17074): (sterile alpha and TIR motif containing 1) Enables NAD+ nucleotidase, cyclic ADP-ribose generating and identical protein binding activity. Involved in NAD catabolic process; positive regulation of neuron death; and response to axon injury. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLC46A1 | NM_080669.6 | c.*4634_*4635dupTT | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000612814.5 | NP_542400.2 | ||
| SARM1 | NM_015077.4 | c.1924-874_1924-873dupAA | intron_variant | Intron 7 of 8 | ENST00000585482.6 | NP_055892.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC46A1 | ENST00000612814.5 | c.*4634_*4635dupTT | 3_prime_UTR_variant | Exon 5 of 5 | 2 | NM_080669.6 | ENSP00000480703.1 | |||
| SARM1 | ENST00000585482.6 | c.1924-874_1924-873dupAA | intron_variant | Intron 7 of 8 | 1 | NM_015077.4 | ENSP00000468032.2 |
Frequencies
GnomAD3 genomes 0.00110 AC: 162AN: 147628Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
162
AN:
147628
Hom.:
Cov.:
0
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 0.00110 AC: 163AN: 147702Hom.: 0 Cov.: 0 AF XY: 0.00132 AC XY: 95AN XY: 71748 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
163
AN:
147702
Hom.:
Cov.:
0
AF XY:
AC XY:
95
AN XY:
71748
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
35
AN:
40248
American (AMR)
AF:
AC:
20
AN:
14894
Ashkenazi Jewish (ASJ)
AF:
AC:
4
AN:
3440
East Asian (EAS)
AF:
AC:
3
AN:
5100
South Asian (SAS)
AF:
AC:
3
AN:
4638
European-Finnish (FIN)
AF:
AC:
21
AN:
9292
Middle Eastern (MID)
AF:
AC:
1
AN:
288
European-Non Finnish (NFE)
AF:
AC:
73
AN:
66844
Other (OTH)
AF:
AC:
3
AN:
2060
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.380
Heterozygous variant carriers
0
11
22
34
45
56
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital defect of folate absorption Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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