18-45730348-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.28G>A(p.Val10Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00426 in 1,613,198 control chromosomes in the GnomAD database, including 152 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 68 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 84 hom. )
Consequence
SLC14A1
NM_015865.7 missense
NM_015865.7 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: -2.13
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0014895201).
BP6
?
Variant 18-45730348-G-A is Benign according to our data. Variant chr18-45730348-G-A is described in ClinVar as [Benign]. Clinvar id is 773341.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.056 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC14A1 | NM_015865.7 | c.28G>A | p.Val10Met | missense_variant | 3/10 | ENST00000321925.9 | |
LOC105372093 | XR_935423.3 | n.826+7118C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC14A1 | ENST00000321925.9 | c.28G>A | p.Val10Met | missense_variant | 3/10 | 1 | NM_015865.7 | P1 | |
ENST00000589510.5 | n.160+7118C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0179 AC: 2719AN: 151730Hom.: 67 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
2719
AN:
151730
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00569 AC: 1430AN: 251288Hom.: 33 AF XY: 0.00451 AC XY: 612AN XY: 135800
GnomAD3 exomes
AF:
AC:
1430
AN:
251288
Hom.:
AF XY:
AC XY:
612
AN XY:
135800
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00284 AC: 4156AN: 1461352Hom.: 84 Cov.: 31 AF XY: 0.00265 AC XY: 1924AN XY: 727004
GnomAD4 exome
AF:
AC:
4156
AN:
1461352
Hom.:
Cov.:
31
AF XY:
AC XY:
1924
AN XY:
727004
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0179 AC: 2723AN: 151846Hom.: 68 Cov.: 32 AF XY: 0.0177 AC XY: 1311AN XY: 74260
GnomAD4 genome
?
AF:
AC:
2723
AN:
151846
Hom.:
Cov.:
32
AF XY:
AC XY:
1311
AN XY:
74260
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
4
ALSPAC
AF:
AC:
2
ESP6500AA
AF:
AC:
227
ESP6500EA
AF:
AC:
9
ExAC
?
AF:
AC:
796
EpiCase
AF:
EpiControl
AF:
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 23, 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
N
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;N;.;.;N;.
MutationTaster
Benign
N;N;N;N;N;N;N;N;N
PrimateAI
Benign
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
0.11
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at