Genetic Variant SLC14A1:c.-22+2268C>T (chr18-45727281-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_001128588.4(SLC14A1):c.10C>T(p.Arg4Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,550,698 control chromosomes in the GnomAD database, including 178,705 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.42 ( 14177 hom., cov: 33)

Exomes 𝑓: 0.48 ( 164528 hom. )

Consequence

SLC14A1
NM_001128588.4 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.597

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=3.8799644E-4).

BP6

Variant 18-45727281-C-T is Benign according to our data. Variant chr18-45727281-C-T is described in ClinVar as [Benign]. Clinvar id is 3060924.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7 link	c.-22+2268C>T		intron_variant	Intron 2 of 9	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.-22+2268C>T		intron_variant	Intron 2 of 9	1	NM_015865.7	ENSP00000318546.4		Q13336-1

Frequencies

GnomAD3 genomes

AF:

0.416

AC:

63251

AN:

151970

Hom.:

14179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.443

GnomAD3 exomes

AF:

0.474

AC:

73007

AN:

153972

Hom.:

17689

AF XY:

0.472

AC XY:

38523

AN XY:

81700

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.512

Gnomad ASJ exome

AF:

0.447

Gnomad EAS exome

AF:

0.538

Gnomad SAS exome

AF:

0.426

Gnomad FIN exome

AF:

0.497

Gnomad NFE exome

AF:

0.495

Gnomad OTH exome

AF:

0.481

GnomAD4 exome

AF:

0.482

AC:

674572

AN:

1398610

Hom.:

164528

Cov.:

AF XY:

0.481

AC XY:

331592

AN XY:

689858

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.512

Gnomad4 ASJ exome

AF:

0.448

Gnomad4 EAS exome

AF:

0.542

Gnomad4 SAS exome

AF:

0.431

Gnomad4 FIN exome

AF:

0.499

Gnomad4 NFE exome

AF:

0.492

Gnomad4 OTH exome

AF:

0.464

GnomAD4 genome

AF:

0.416

AC:

63259

AN:

152088

Hom.:

14177

Cov.:

AF XY:

0.415

AC XY:

30842

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.234

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.518

Gnomad4 SAS

AF:

0.414

Gnomad4 FIN

AF:

0.489

Gnomad4 NFE

AF:

0.493

Gnomad4 OTH

AF:

0.441

Alfa

AF:

0.461

Hom.:

13408

Bravo

AF:

0.409

TwinsUK

AF:

0.481

AC:

1784

ALSPAC

AF:

0.489

AC:

1886

ESP6500AA

AF:

0.212

AC:

293

ESP6500EA

AF:

0.492

AC:

1567

ExAC

AF:

0.416

AC:

9149

Asia WGS

AF:

0.430

AC:

1500

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC14A1-related disorder

Benign:1

Oct 17, 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

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

-0.026

Eigen_PC

Benign

-0.070

FATHMM_MKL

Benign

0.22

LIST_S2

Benign

0.74

.;T

MetaRNN

Benign

0.00039

T;T

MetaSVM

Benign

-0.91

PrimateAI

Benign

0.26

PROVEAN

Benign

-1.4

N;N

REVEL

Benign

0.084

Sift

Uncertain

0.0020

D;D

Sift4G

Uncertain

0.0020

D;D

Polyphen

0.99

D;D

Vest4

0.074

MPC

0.11

ClinPred

0.019

GERP RS

2.8

gMVP

0.12

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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