8-86214637-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_138817.3(SLC7A13):ā€‹c.1189T>Cā€‹(p.Ser397Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000386 in 1,606,100 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.0012 ( 1 hom., cov: 33)
Exomes š‘“: 0.00030 ( 4 hom. )

Consequence

SLC7A13
NM_138817.3 missense

Scores

18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.94
Variant links:
Genes affected
SLC7A13 (HGNC:23092): (solute carrier family 7 member 13) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-cystine transport; L-glutamate transmembrane transport; and aspartate transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.004819691).
BP6
Variant 8-86214637-A-G is Benign according to our data. Variant chr8-86214637-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2055187.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC7A13NM_138817.3 linkc.1189T>C p.Ser397Pro missense_variant 4/4 ENST00000297524.8 NP_620172.2 Q8TCU3-1
SLC7A13XM_011516867.3 linkc.1162T>C p.Ser388Pro missense_variant 4/4 XP_011515169.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC7A13ENST00000297524.8 linkc.1189T>C p.Ser397Pro missense_variant 4/41 NM_138817.3 ENSP00000297524.3 Q8TCU3-1
SLC7A13ENST00000419776.2 linkc.1290T>C p.Cys430Cys synonymous_variant 5/51 ENSP00000410982.2 Q8TCU3-2

Frequencies

GnomAD3 genomes
AF:
0.00112
AC:
170
AN:
152228
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00359
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.000303
AC:
74
AN:
244278
Hom.:
0
AF XY:
0.000159
AC XY:
21
AN XY:
132262
show subpopulations
Gnomad AFR exome
AF:
0.00397
Gnomad AMR exome
AF:
0.0000910
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000362
Gnomad OTH exome
AF:
0.000504
GnomAD4 exome
AF:
0.000303
AC:
440
AN:
1453754
Hom.:
4
Cov.:
31
AF XY:
0.000313
AC XY:
226
AN XY:
722590
show subpopulations
Gnomad4 AFR exome
AF:
0.00503
Gnomad4 AMR exome
AF:
0.0000928
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000586
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000173
Gnomad4 OTH exome
AF:
0.00100
GnomAD4 genome
AF:
0.00118
AC:
180
AN:
152346
Hom.:
1
Cov.:
33
AF XY:
0.00105
AC XY:
78
AN XY:
74502
show subpopulations
Gnomad4 AFR
AF:
0.00382
Gnomad4 AMR
AF:
0.000261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.000336
Hom.:
0
Bravo
AF:
0.00126
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00545
AC:
24
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000445
AC:
54
Asia WGS
AF:
0.00231
AC:
8
AN:
3476
EpiCase
AF:
0.000220
EpiControl
AF:
0.000119

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 03, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.041
BayesDel_addAF
Benign
-0.40
T
BayesDel_noAF
Benign
-0.35
CADD
Benign
8.6
DANN
Benign
0.89
DEOGEN2
Benign
0.069
T
Eigen
Benign
-1.0
Eigen_PC
Benign
-0.87
FATHMM_MKL
Benign
0.0022
N
LIST_S2
Benign
0.18
T
M_CAP
Benign
0.051
D
MetaRNN
Benign
0.0048
T
MetaSVM
Benign
-0.75
T
PrimateAI
Benign
0.28
T
PROVEAN
Benign
2.8
N
REVEL
Benign
0.21
Sift
Benign
0.92
T
Sift4G
Benign
0.91
T
Polyphen
0.0010
B
Vest4
0.093
MVP
0.24
MPC
0.0079
ClinPred
0.013
T
GERP RS
4.3
Varity_R
0.045
gMVP
0.45

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs74736195; hg19: chr8-87226866; API