rs1444590

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_030674.4(SLC38A1):​c.647-435A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,112 control chromosomes in the GnomAD database, including 3,534 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 3534 hom., cov: 32)

Consequence

SLC38A1
NM_030674.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430

Publications

1 publications found
Variant links:
Genes affected
SLC38A1 (HGNC:13447): (solute carrier family 38 member 1) Amino acid transporters play essential roles in the uptake of nutrients, production of energy, chemical metabolism, detoxification, and neurotransmitter cycling. SLC38A1 is an important transporter of glutamine, an intermediate in the detoxification of ammonia and the production of urea. Glutamine serves as a precursor for the synaptic transmitter, glutamate (Gu et al., 2001 [PubMed 11325958]).[supplied by OMIM, Mar 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030674.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC38A1
NM_030674.4
MANE Select
c.647-435A>G
intron
N/ANP_109599.3
SLC38A1
NM_001278390.1
c.647-435A>G
intron
N/ANP_001265319.1F8VX04
SLC38A1
NM_001077484.2
c.647-435A>G
intron
N/ANP_001070952.1Q9H2H9

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC38A1
ENST00000398637.10
TSL:1 MANE Select
c.647-435A>G
intron
N/AENSP00000381634.4Q9H2H9
SLC38A1
ENST00000552197.5
TSL:1
c.647-435A>G
intron
N/AENSP00000449756.1F8VX04
SLC38A1
ENST00000439706.5
TSL:1
c.647-435A>G
intron
N/AENSP00000398142.1Q9H2H9

Frequencies

GnomAD3 genomes
AF:
0.193
AC:
29339
AN:
151994
Hom.:
3529
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.343
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.137
Gnomad ASJ
AF:
0.124
Gnomad EAS
AF:
0.0859
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.111
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.143
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29369
AN:
152112
Hom.:
3534
Cov.:
32
AF XY:
0.189
AC XY:
14069
AN XY:
74362
show subpopulations
African (AFR)
AF:
0.343
AC:
14214
AN:
41456
American (AMR)
AF:
0.137
AC:
2097
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.124
AC:
429
AN:
3468
East Asian (EAS)
AF:
0.0859
AC:
444
AN:
5166
South Asian (SAS)
AF:
0.152
AC:
733
AN:
4832
European-Finnish (FIN)
AF:
0.111
AC:
1180
AN:
10590
Middle Eastern (MID)
AF:
0.190
AC:
56
AN:
294
European-Non Finnish (NFE)
AF:
0.143
AC:
9699
AN:
67996
Other (OTH)
AF:
0.190
AC:
401
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1146
2292
3438
4584
5730
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
306
612
918
1224
1530
<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:
0.170
Hom.:
992
Bravo
AF:
0.199
Asia WGS
AF:
0.129
AC:
451
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
6.2
DANN
Benign
0.68
PhyloP100
-0.43
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1444590; hg19: chr12-46598808; API
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.