18-45731089-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015865.7(SLC14A1):c.226G>A(p.Val76Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0052 in 1,614,142 control chromosomes in the GnomAD database, including 234 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 111 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 123 hom. )
Consequence
SLC14A1
NM_015865.7 missense
NM_015865.7 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 1.71
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=0.0046189725).
BP6
?
Variant 18-45731089-G-A is Benign according to our data. Variant chr18-45731089-G-A is described in ClinVar as [Benign]. Clinvar id is 773342.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0691 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC14A1 | NM_015865.7 | c.226G>A | p.Val76Ile | missense_variant | 4/10 | ENST00000321925.9 | |
LOC105372093 | XR_935423.3 | n.826+6377C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC14A1 | ENST00000321925.9 | c.226G>A | p.Val76Ile | missense_variant | 4/10 | 1 | NM_015865.7 | P1 | |
ENST00000589510.5 | n.160+6377C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0220 AC: 3340AN: 152158Hom.: 110 Cov.: 32
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GnomAD3 exomes AF: 0.00692 AC: 1740AN: 251428Hom.: 47 AF XY: 0.00542 AC XY: 737AN XY: 135880
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GnomAD4 exome AF: 0.00345 AC: 5042AN: 1461866Hom.: 123 Cov.: 32 AF XY: 0.00324 AC XY: 2356AN XY: 727232
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GnomAD4 genome ? AF: 0.0220 AC: 3346AN: 152276Hom.: 111 Cov.: 32 AF XY: 0.0217 AC XY: 1612AN XY: 74454
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ESP6500AA
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281
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ExAC
?
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986
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.;T;.;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;N;.;.;N;.
MutationTaster
Benign
D;D;D;D;N;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;.;.;N;.;.
REVEL
Benign
Sift
Benign
T;.;T;.;.;T;.;.
Sift4G
Benign
T;T;T;T;T;T;T;T
Polyphen
B;.;B;B;.;B;B;.
Vest4
MVP
MPC
0.084
ClinPred
T
GERP RS
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gMVP
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