rs2298720
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015865.7(SLC14A1):c.130G>A(p.Glu44Lys) variant causes a missense change. The variant allele was found at a frequency of 0.102 in 1,613,960 control chromosomes in the GnomAD database, including 13,402 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.14 ( 1962 hom., cov: 32)
Exomes 𝑓: 0.099 ( 11440 hom. )
Consequence
SLC14A1
NM_015865.7 missense
NM_015865.7 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 4.35
Genes affected
SLC14A1 (HGNC:10918): (solute carrier family 14 member 1 (Kidd blood group)) The protein encoded by this gene is a membrane transporter that mediates urea transport in erythrocytes. This gene forms the basis for the Kidd blood group system. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.00406754).
BP6
Variant 18-45730450-G-A is Benign according to our data. Variant chr18-45730450-G-A is described in ClinVar as [Benign]. Clinvar id is 3059300.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC14A1 | NM_015865.7 | c.130G>A | p.Glu44Lys | missense_variant | 3/10 | ENST00000321925.9 | |
LOC105372093 | XR_935423.3 | n.826+7016C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC14A1 | ENST00000321925.9 | c.130G>A | p.Glu44Lys | missense_variant | 3/10 | 1 | NM_015865.7 | P1 | |
ENST00000589510.5 | n.160+7016C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.138 AC: 20915AN: 152026Hom.: 1959 Cov.: 32
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GnomAD3 exomes AF: 0.152 AC: 38188AN: 251310Hom.: 4241 AF XY: 0.148 AC XY: 20132AN XY: 135812
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GnomAD4 exome AF: 0.0988 AC: 144449AN: 1461816Hom.: 11440 Cov.: 32 AF XY: 0.102 AC XY: 74446AN XY: 727212
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GnomAD4 genome AF: 0.138 AC: 20943AN: 152144Hom.: 1962 Cov.: 32 AF XY: 0.145 AC XY: 10772AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC14A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;T;.;.;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;.;.;T;T;T;.
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;.;.;M;.;.;M;.
MutationTaster
Benign
P;P;P;P;P;P;P;P;P
PrimateAI
Benign
T
PROVEAN
Uncertain
D;.;D;.;.;D;.;.
REVEL
Benign
Sift
Uncertain
D;.;D;.;.;D;.;.
Sift4G
Uncertain
D;D;D;D;D;D;D;D
Polyphen
B;.;P;B;.;P;B;.
Vest4
MPC
0.33
ClinPred
T
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Splicing
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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