7-123134504-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_022444.4(SLC13A1):c.838A>G(p.Asn280Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000725 in 1,613,424 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: đť‘“ 0.000046 ( 0 hom., cov: 32)
Exomes đť‘“: 0.000075 ( 3 hom. )
Consequence
SLC13A1
NM_022444.4 missense
NM_022444.4 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 5.76
Genes affected
SLC13A1 (HGNC:10916): (solute carrier family 13 member 1) The protein encoded by this gene is an apical membrane Na(+)-sulfate cotransporter involved in sulfate homeostasis in the kidney. Defects in this gene lead to many pathophysiologic problems. [provided by RefSeq, May 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
?
Variant 7-123134504-T-C is Benign according to our data. Variant chr7-123134504-T-C is described in ClinVar as [Benign]. Clinvar id is 208971.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC13A1 | NM_022444.4 | c.838A>G | p.Asn280Asp | missense_variant | 8/15 | ENST00000194130.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC13A1 | ENST00000194130.7 | c.838A>G | p.Asn280Asp | missense_variant | 8/15 | 1 | NM_022444.4 | P1 | |
SLC13A1 | ENST00000439260.5 | c.*1216A>G | 3_prime_UTR_variant, NMD_transcript_variant | 11/18 | 1 | ||||
SLC13A1 | ENST00000539873.1 | c.*505A>G | 3_prime_UTR_variant | 9/16 | 5 | ||||
SLC13A1 | ENST00000427975.5 | c.*781A>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/16 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152122Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
7
AN:
152122
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:
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250796Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135570
GnomAD3 exomes
AF:
AC:
8
AN:
250796
Hom.:
AF XY:
AC XY:
4
AN XY:
135570
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1461184Hom.: 3 Cov.: 30 AF XY: 0.0000867 AC XY: 63AN XY: 726878
GnomAD4 exome
AF:
AC:
110
AN:
1461184
Hom.:
Cov.:
30
AF XY:
AC XY:
63
AN XY:
726878
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74440
GnomAD4 genome
?
AF:
AC:
7
AN:
152240
Hom.:
Cov.:
32
AF XY:
AC XY:
5
AN XY:
74440
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
?
AF:
AC:
4
Asia WGS
AF:
AC:
2
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Abnormality of neuronal migration Benign:1
Benign, no assertion criteria provided | clinical testing | Génétique et pathophysiologie de maladies neurodéveloppementales et épileptogènes, Institut de génétique et de biologie moléculaire et cellulaire | Oct 31, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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