chr19-33208962-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_019849.3(SLC7A10):​c.1501G>A​(p.Glu501Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

SLC7A10
NM_019849.3 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.155
Variant links:
Genes affected
SLC7A10 (HGNC:11058): (solute carrier family 7 member 10) SLC7A10, in association with 4F2HC (SLC3A2; MIM 158070), mediates high-affinity transport of D-serine and several other neutral amino acids (Nakauchi et al., 2000 [PubMed 10863037]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17183578).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC7A10NM_019849.3 linkuse as main transcriptc.1501G>A p.Glu501Lys missense_variant 11/11 ENST00000253188.8 NP_062823.1 Q9NS82

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC7A10ENST00000253188.8 linkuse as main transcriptc.1501G>A p.Glu501Lys missense_variant 11/111 NM_019849.3 ENSP00000253188.2 Q9NS82
SLC7A10ENST00000590036.5 linkuse as main transcriptn.*234G>A non_coding_transcript_exon_variant 10/105 ENSP00000465421.1 K7EK24
SLC7A10ENST00000590490.1 linkuse as main transcriptn.1276G>A non_coding_transcript_exon_variant 4/42
SLC7A10ENST00000590036.5 linkuse as main transcriptn.*234G>A 3_prime_UTR_variant 10/105 ENSP00000465421.1 K7EK24

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000798
AC:
2
AN:
250750
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135670
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.0000994
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.00000479
AC:
7
AN:
1461520
Hom.:
0
Cov.:
36
AF XY:
0.00000550
AC XY:
4
AN XY:
727058
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.0000264

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsOct 17, 2024The c.1501G>A (p.E501K) alteration is located in exon 11 (coding exon 11) of the SLC7A10 gene. This alteration results from a G to A substitution at nucleotide position 1501, causing the glutamic acid (E) at amino acid position 501 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.081
BayesDel_addAF
Uncertain
0.041
T
BayesDel_noAF
Benign
-0.18
CADD
Benign
17
DANN
Uncertain
0.99
DEOGEN2
Benign
0.088
T
Eigen
Benign
-0.48
Eigen_PC
Benign
-0.41
FATHMM_MKL
Benign
0.28
N
LIST_S2
Benign
0.71
T
M_CAP
Benign
0.077
D
MetaRNN
Benign
0.17
T
MetaSVM
Benign
-0.34
T
MutationAssessor
Benign
2.0
M
PrimateAI
Benign
0.43
T
PROVEAN
Benign
-0.64
N
REVEL
Uncertain
0.33
Sift
Benign
0.35
T
Sift4G
Benign
0.25
T
Polyphen
0.013
B
Vest4
0.31
MutPred
0.39
Gain of methylation at E501 (P = 0.0022);
MVP
0.83
MPC
0.43
ClinPred
0.15
T
GERP RS
4.9
Varity_R
0.14
gMVP
0.52

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: rs1429134939; hg19: chr19-33699868; API