chr1-94820962-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001114106.3(SLC44A3):c.41G>C(p.Gly14Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000953 in 1,551,000 control chromosomes in the GnomAD database, including 3 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00064 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00099 ( 1 hom. )
Consequence
SLC44A3
NM_001114106.3 missense
NM_001114106.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.656
Genes affected
SLC44A3 (HGNC:28689): (solute carrier family 44 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005376041).
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC44A3 | NM_001114106.3 | c.41G>C | p.Gly14Ala | missense_variant | 2/15 | ENST00000271227.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A3 | ENST00000271227.11 | c.41G>C | p.Gly14Ala | missense_variant | 2/15 | 1 | NM_001114106.3 | P1 | |
SLC44A3-AS1 | ENST00000634339.1 | n.178+34282C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000644 AC: 98AN: 152130Hom.: 2 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000518 AC: 81AN: 156468Hom.: 0 AF XY: 0.000494 AC XY: 41AN XY: 82934
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GnomAD4 exome AF: 0.000987 AC: 1381AN: 1398752Hom.: 1 Cov.: 31 AF XY: 0.000984 AC XY: 679AN XY: 689914
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GnomAD4 genome ? AF: 0.000637 AC: 97AN: 152248Hom.: 2 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74440
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ExAC
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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 submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.41G>C (p.G14A) alteration is located in exon 2 (coding exon 2) of the SLC44A3 gene. This alteration results from a G to C substitution at nucleotide position 41, causing the glycine (G) at amino acid position 14 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at