Variant rs77474263 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018242.3(SLC47A1):c.373C>T(p.Leu125Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00518 in 1,614,144 control chromosomes in the GnomAD database, including 523 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0082 ( 59 hom., cov: 31)

Exomes 𝑓: 0.0049 ( 464 hom. )

Consequence

SLC47A1
NM_018242.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.71

Variant links:

Genes affected

SLC47A1 (HGNC:25588): (solute carrier family 47 member 1) This gene is located within the Smith-Magenis syndrome region on chromosome 17. It encodes a protein of unknown function. [provided by RefSeq, Jul 2008]

SLC47A1 links:

SLC47A1 (HGNC:):

SLC47A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0039165616).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A1	NM_018242.3 linkuse as main transcript	c.373C>T	p.Leu125Phe	missense_variant	4/17	ENST00000270570.8	NP_060712.2	Q96FL8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A1	ENST00000270570.8 linkuse as main transcript	c.373C>T	p.Leu125Phe	missense_variant	4/17	1	NM_018242.3	ENSP00000270570.4		Q96FL8-1

Frequencies

GnomAD3 genomes

AF:

0.00818

AC:

1245

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000748

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0696

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.00347

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00471

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.00814

GnomAD3 exomes

AF:

0.0209

AC:

5259

AN:

251360

Hom.:

389

AF XY:

0.0157

AC XY:

2136

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.139

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.00516

Gnomad SAS exome

AF:

0.000621

Gnomad FIN exome

AF:

0.00486

Gnomad NFE exome

AF:

0.000290

Gnomad OTH exome

AF:

0.0143

GnomAD4 exome

AF:

0.00487

AC:

7119

AN:

1461832

Hom.:

464

Cov.:

AF XY:

0.00417

AC XY:

3030

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.000836

Gnomad4 AMR exome

AF:

0.130

Gnomad4 ASJ exome

AF:

0.0109

Gnomad4 EAS exome

AF:

0.00731

Gnomad4 SAS exome

AF:

0.000742

Gnomad4 FIN exome

AF:

0.00480

Gnomad4 NFE exome

AF:

0.000107

Gnomad4 OTH exome

AF:

0.00401

GnomAD4 genome

AF:

0.00820

AC:

1249

AN:

152312

Hom.:

Cov.:

AF XY:

0.00990

AC XY:

737

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.000745

Gnomad4 AMR

AF:

0.0698

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.00347

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00471

Gnomad4 NFE

AF:

0.000250

Gnomad4 OTH

AF:

0.00806

Alfa

AF:

0.00259

Hom.:

Bravo

AF:

0.0132

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00116

AC:

ExAC

AF:

0.0157

AC:

1901

Asia WGS

AF:

0.00635

AC:

AN:

3478

EpiCase

AF:

0.000382

EpiControl

AF:

0.000415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.090

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.049

T;T;.;.

Eigen

Uncertain

0.63

Eigen_PC

Uncertain

0.54

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.95

D;D;D;D

MetaRNN

Benign

0.0039

T;T;T;T

MetaSVM

Benign

-0.88

MutationAssessor

Pathogenic

3.0

.;M;.;M

PrimateAI

Uncertain

0.51

PROVEAN

Uncertain

-3.9

D;D;.;D

REVEL

Uncertain

0.44

Sift

Uncertain

0.0030

D;D;.;D

Sift4G

Pathogenic

0.0

D;D;D;D

Polyphen

1.0

D;D;.;D

Vest4

0.39

MPC

0.72

ClinPred

0.022

GERP RS

4.0

Varity_R

0.57

gMVP

0.42

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over