18-45736496-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015865.7(SLC14A1):c.511T>C(p.Trp171Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0008 in 1,614,206 control chromosomes in the GnomAD database, including 5 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 0.0041 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00045 ( 5 hom. )
Consequence
SLC14A1
NM_015865.7 missense
NM_015865.7 missense
Scores
6
5
6
Clinical Significance
Conservation
PhyloP100: 7.10
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.011821806).
BP6
?
Variant 18-45736496-T-C is Benign according to our data. Variant chr18-45736496-T-C is described in ClinVar as [Benign]. Clinvar id is 769937.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 4 BG gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC14A1 | NM_015865.7 | c.511T>C | p.Trp171Arg | missense_variant | 6/10 | ENST00000321925.9 | |
LOC105372093 | XR_935423.3 | n.826+970A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC14A1 | ENST00000321925.9 | c.511T>C | p.Trp171Arg | missense_variant | 6/10 | 1 | NM_015865.7 | P1 | |
ENST00000589510.5 | n.160+970A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00409 AC: 623AN: 152204Hom.: 0 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
623
AN:
152204
Hom.:
Cov.:
33
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: 0.00115 AC: 290AN: 251428Hom.: 4 AF XY: 0.000905 AC XY: 123AN XY: 135886
GnomAD3 exomes
AF:
AC:
290
AN:
251428
Hom.:
AF XY:
AC XY:
123
AN XY:
135886
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: 0.000454 AC: 663AN: 1461884Hom.: 5 Cov.: 32 AF XY: 0.000419 AC XY: 305AN XY: 727246
GnomAD4 exome
AF:
AC:
663
AN:
1461884
Hom.:
Cov.:
32
AF XY:
AC XY:
305
AN XY:
727246
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: 0.00412 AC: 628AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.00406 AC XY: 302AN XY: 74466
GnomAD4 genome
?
AF:
AC:
628
AN:
152322
Hom.:
Cov.:
33
AF XY:
AC XY:
302
AN XY:
74466
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:
ESP6500AA
AF:
AC:
68
ESP6500EA
AF:
AC:
0
ExAC
?
AF:
AC:
183
Asia WGS
AF:
AC:
3
AN:
3478
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 | Dec 11, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;T;T;.;.;T;.;.;.;.;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;.;.;.;.;M;.;.;.;.;M;.
MutationTaster
Benign
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;.;D;D;.;.;D;D;D;.;.;.
REVEL
Uncertain
Sift
Pathogenic
D;.;D;D;.;.;D;D;D;.;.;.
Sift4G
Pathogenic
D;D;D;D;D;.;D;D;D;D;D;D
Polyphen
D;.;B;D;.;D;.;.;D;.;D;.
Vest4
MutPred
Gain of disorder (P = 0.0141);Gain of disorder (P = 0.0141);.;.;.;Gain of disorder (P = 0.0141);.;.;.;.;Gain of disorder (P = 0.0141);Gain of disorder (P = 0.0141);
MVP
MPC
0.66
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