rs769484443

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_032839.3(SLC49A4):​c.238C>G​(p.Arg80Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R80C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

SLC49A4
NM_032839.3 missense

Scores

1
7
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21
Variant links:
Genes affected
SLC49A4 (HGNC:16628): (solute carrier family 49 member 4) This gene encodes a membrane-bound protein from the major facilitator superfamily of transporters. Disruption of this gene by translocation has been associated with haplo-insufficiency and renal cell carcinomas. Alternatively spliced transcript variants have been described, but their biological validity has not yet been determined. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.38774133).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC49A4NM_032839.3 linkc.238C>G p.Arg80Gly missense_variant Exon 1 of 9 ENST00000261038.6 NP_116228.1 Q96SL1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC49A4ENST00000261038.6 linkc.238C>G p.Arg80Gly missense_variant Exon 1 of 9 1 NM_032839.3 ENSP00000261038.5 Q96SL1-1
SLC49A4ENST00000477647.1 linkn.238C>G non_coding_transcript_exon_variant Exon 1 of 8 1 ENSP00000418554.1 Q05BS2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.87e-7
AC:
1
AN:
1455668
Hom.:
0
Cov.:
34
AF XY:
0.00000138
AC XY:
1
AN XY:
724318
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Uncertain
-0.060
CADD
Benign
23
DANN
Uncertain
0.99
Eigen
Benign
-0.22
Eigen_PC
Benign
-0.048
FATHMM_MKL
Benign
0.54
D
LIST_S2
Uncertain
0.87
D
M_CAP
Pathogenic
0.50
D
MetaRNN
Benign
0.39
T
MetaSVM
Uncertain
-0.15
T
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-1.8
N
REVEL
Uncertain
0.43
Sift
Benign
0.16
T
Sift4G
Benign
0.074
T
Vest4
0.44
MutPred
0.60
Loss of stability (P = 0.0512);
MVP
0.53
MPC
0.39
ClinPred
0.61
D
GERP RS
4.3
gMVP
0.65

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-122514277; API