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GeneBe

18-45736573-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_015865.7(SLC14A1):c.588A>G(p.Pro196=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 1,613,580 control chromosomes in the GnomAD database, including 280,703 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.61 ( 29070 hom., cov: 32)
Exomes 𝑓: 0.58 ( 251633 hom. )

Consequence

SLC14A1
NM_015865.7 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.94
Variant links:
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 18-45736573-A-G is Benign according to our data. Variant chr18-45736573-A-G is described in ClinVar as [Benign]. Clinvar id is 3059083.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.94 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC14A1NM_015865.7 linkuse as main transcriptc.588A>G p.Pro196= synonymous_variant 6/10 ENST00000321925.9
LOC105372093XR_935423.3 linkuse as main transcriptn.826+893T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC14A1ENST00000321925.9 linkuse as main transcriptc.588A>G p.Pro196= synonymous_variant 6/101 NM_015865.7 P1Q13336-1
ENST00000589510.5 linkuse as main transcriptn.160+893T>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.612
AC:
93047
AN:
151948
Hom.:
29044
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.649
Gnomad AMI
AF:
0.399
Gnomad AMR
AF:
0.689
Gnomad ASJ
AF:
0.521
Gnomad EAS
AF:
0.928
Gnomad SAS
AF:
0.679
Gnomad FIN
AF:
0.593
Gnomad MID
AF:
0.547
Gnomad NFE
AF:
0.555
Gnomad OTH
AF:
0.598
GnomAD3 exomes
AF:
0.638
AC:
160446
AN:
251422
Hom.:
52822
AF XY:
0.631
AC XY:
85790
AN XY:
135888
show subpopulations
Gnomad AFR exome
AF:
0.653
Gnomad AMR exome
AF:
0.763
Gnomad ASJ exome
AF:
0.530
Gnomad EAS exome
AF:
0.930
Gnomad SAS exome
AF:
0.684
Gnomad FIN exome
AF:
0.599
Gnomad NFE exome
AF:
0.557
Gnomad OTH exome
AF:
0.605
GnomAD4 exome
AF:
0.581
AC:
848894
AN:
1461514
Hom.:
251633
Cov.:
49
AF XY:
0.582
AC XY:
423457
AN XY:
727074
show subpopulations
Gnomad4 AFR exome
AF:
0.651
Gnomad4 AMR exome
AF:
0.754
Gnomad4 ASJ exome
AF:
0.527
Gnomad4 EAS exome
AF:
0.934
Gnomad4 SAS exome
AF:
0.684
Gnomad4 FIN exome
AF:
0.598
Gnomad4 NFE exome
AF:
0.551
Gnomad4 OTH exome
AF:
0.591
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.612
AC:
93122
AN:
152066
Hom.:
29070
Cov.:
32
AF XY:
0.615
AC XY:
45747
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.649
Gnomad4 AMR
AF:
0.690
Gnomad4 ASJ
AF:
0.521
Gnomad4 EAS
AF:
0.928
Gnomad4 SAS
AF:
0.678
Gnomad4 FIN
AF:
0.593
Gnomad4 NFE
AF:
0.555
Gnomad4 OTH
AF:
0.596
Alfa
AF:
0.572
Hom.:
60375
Bravo
AF:
0.621
Asia WGS
AF:
0.770
AC:
2679
AN:
3478
EpiCase
AF:
0.547
EpiControl
AF:
0.553

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 submitterclinical testingPreventionGenetics, part of Exact SciencesOct 17, 2019This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.13
Dann
Benign
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2298718; hg19: chr18-43316538; COSMIC: COSV58934706; COSMIC: COSV58934706; API