rs1870852593

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_182767.6(SLC6A15):​c.2165T>G​(p.Met722Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M722T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

SLC6A15
NM_182767.6 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

0 publications found
Variant links:
Genes affected
SLC6A15 (HGNC:13621): (solute carrier family 6 member 15) This gene encodes a member of the solute carrier family 6 protein family which transports neutral amino acids. The encoded protein is thought to play a role in neuronal amino acid transport (PMID: 16185194) and may be associated with major depression (PMID: 21521612). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1859647).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC6A15NM_182767.6 linkc.2165T>G p.Met722Arg missense_variant Exon 12 of 12 ENST00000266682.10 NP_877499.1 Q9H2J7-1
SLC6A15NM_001146335.3 linkc.1844T>G p.Met615Arg missense_variant Exon 11 of 11 NP_001139807.1 Q9H2J7-3Q9NW50Q8IXG2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC6A15ENST00000266682.10 linkc.2165T>G p.Met722Arg missense_variant Exon 12 of 12 1 NM_182767.6 ENSP00000266682.5 Q9H2J7-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
0.0023
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
20
DANN
Benign
0.89
DEOGEN2
Benign
0.12
T;.
Eigen
Benign
-0.16
Eigen_PC
Benign
-0.26
FATHMM_MKL
Uncertain
0.83
D
LIST_S2
Benign
0.42
T;T
M_CAP
Benign
0.052
D
MetaRNN
Benign
0.19
T;T
MetaSVM
Benign
-0.71
T
MutationAssessor
Benign
1.7
L;.
PhyloP100
0.35
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-0.50
N;N
REVEL
Benign
0.26
Sift
Benign
0.058
T;T
Sift4G
Benign
0.10
T;T
Polyphen
0.95
P;.
Vest4
0.41
MutPred
0.27
Gain of catalytic residue at P723 (P = 0.0032);.;
MVP
0.68
MPC
0.55
ClinPred
0.23
T
GERP RS
0.43
Varity_R
0.52
gMVP
0.76
Mutation Taster
=65/35
polymorphism

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: rs1870852593; hg19: chr12-85255439; API