Genetic Variant SLC14A1:p.Glu44Lys (chr18-45730450-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

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 (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.14 ( 1962 hom., cov: 32)

Exomes 𝑓: 0.099 ( 11440 hom. )

Consequence

SLC14A1
NM_015865.7 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 4.35

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]

SLC14A1 links:

ENSG00000288545 (HGNC:):

ENSG00000288545 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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 no_assertion_criteria_provided, 0 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 rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7 link	c.130G>A	p.Glu44Lys	missense_variant	Exon 3 of 10	ENST00000321925.9	NP_056949.4	Q13336-1G0W2N5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9 link	c.130G>A	p.Glu44Lys	missense_variant	Exon 3 of 10	1	NM_015865.7	ENSP00000318546.4		Q13336-1

Frequencies

GnomAD3 genomes

AF:

0.138

AC:

20915

AN:

152026

Hom.:

1959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.406

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0679

Gnomad OTH

AF:

0.113

GnomAD3 exomes

AF:

0.152

AC:

38188

AN:

251310

Hom.:

4241

AF XY:

0.148

AC XY:

20132

AN XY:

135812

show subpopulations

Gnomad AFR exome

AF:

0.200

Gnomad AMR exome

AF:

0.235

Gnomad ASJ exome

AF:

0.102

Gnomad EAS exome

AF:

0.392

Gnomad SAS exome

AF:

0.257

Gnomad FIN exome

AF:

0.119

Gnomad NFE exome

AF:

0.0652

Gnomad OTH exome

AF:

0.120

GnomAD4 exome

AF:

0.0988

AC:

144449

AN:

1461816

Hom.:

11440

Cov.:

AF XY:

0.102

AC XY:

74446

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.199

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.0998

Gnomad4 EAS exome

AF:

0.390

Gnomad4 SAS exome

AF:

0.254

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.0665

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.138

AC:

20943

AN:

152144

Hom.:

1962

Cov.:

AF XY:

0.145

AC XY:

10772

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.197

Gnomad4 AMR

AF:

0.184

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.405

Gnomad4 SAS

AF:

0.268

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.0680

Gnomad4 OTH

AF:

0.113

Alfa

AF:

0.0921

Hom.:

1772

Bravo

AF:

0.143

TwinsUK

AF:

0.0653

AC:

242

ALSPAC

AF:

0.0703

AC:

271

ESP6500AA

AF:

0.193

AC:

849

ESP6500EA

AF:

0.0649

AC:

558

ExAC

AF:

0.147

AC:

17904

Asia WGS

AF:

0.316

AC:

1095

AN:

3478

EpiCase

AF:

0.0663

EpiControl

AF:

0.0680

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC14A1-related disorder

Benign:1

Oct 21, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.40

T;T;.;T;.;.;T;T

Eigen

Uncertain

0.29

Eigen_PC

Uncertain

0.29

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.73

.;T;.;.;T;T;T;.

MetaRNN

Benign

0.0041

T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Pathogenic

3.2

M;.;.;M;.;.;M;.

PrimateAI

Benign

0.47

PROVEAN

Uncertain

-2.7

D;.;D;.;.;D;.;.

REVEL

Benign

0.16

Sift

Uncertain

0.012

D;.;D;.;.;D;.;.

Sift4G

Uncertain

0.026

D;D;D;D;D;D;D;D

Polyphen

0.45

B;.;P;B;.;P;B;.

Vest4

0.43

MPC

0.33

ClinPred

0.050

GERP RS

5.0

Varity_R

0.46

gMVP

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over