19-10631490-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020428.4(SLC44A2):c.457C>T(p.Leu153Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00516 in 1,614,060 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0042 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0053 ( 18 hom. )
Consequence
SLC44A2
NM_020428.4 missense
NM_020428.4 missense
Scores
1
6
11
Clinical Significance
Conservation
PhyloP100: 3.43
Genes affected
SLC44A2 (HGNC:17292): (solute carrier family 44 member 2 (CTL2 blood group)) Enables choline transmembrane transporter activity. Involved in choline transport and transmembrane transport. Located in mitochondrion and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0039951503).
BP6
Variant 19-10631490-C-T is Benign according to our data. Variant chr19-10631490-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649298.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00417 AC: 635AN: 152138Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00430 AC: 1079AN: 251190Hom.: 3 AF XY: 0.00426 AC XY: 578AN XY: 135770
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GnomAD4 exome AF: 0.00526 AC: 7695AN: 1461804Hom.: 18 Cov.: 38 AF XY: 0.00516 AC XY: 3750AN XY: 727210
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GnomAD4 genome AF: 0.00417 AC: 635AN: 152256Hom.: 3 Cov.: 32 AF XY: 0.00365 AC XY: 272AN XY: 74440
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
SLC44A2: BS2 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
.;.;M;.;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;N;N;.;.
REVEL
Benign
Sift
Uncertain
.;D;D;.;.
Sift4G
Benign
T;T;T;D;T
Polyphen
0.15, 0.092
.;B;B;.;.
Vest4
0.28, 0.27, 0.28
MVP
MPC
0.46
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Score
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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