Variant chr1-205659488-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_033102.3(SLC45A3):c.1408G>A(p.Val470Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00795 in 1,613,828 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0064 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0081 ( 67 hom. )

Consequence

SLC45A3
NM_033102.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0110

Variant links:

Genes affected

SLC45A3 (HGNC:8642): (solute carrier family 45 member 3) Predicted to enable sucrose:proton symporter activity. Predicted to be involved in positive regulation of small molecule metabolic process; regulation of oligodendrocyte differentiation; and sucrose transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC45A3 links:

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=0.0025591552).

BP6

Variant 1-205659488-C-T is Benign according to our data. Variant chr1-205659488-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2639855.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC45A3	NM_033102.3 linkuse as main transcript	c.1408G>A	p.Val470Ile	missense_variant	5/5	ENST00000367145.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC45A3	ENST00000367145.4 linkuse as main transcript	c.1408G>A	p.Val470Ile	missense_variant	5/5	1	NM_033102.3	P1
SLC45A3	ENST00000460934.1 linkuse as main transcript	n.811G>A		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes

AF:

0.00643

AC:

978

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00930

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00559

Gnomad FIN

AF:

0.00555

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00938

Gnomad OTH

AF:

0.00861

GnomAD3 exomes

AF:

0.00692

AC:

1731

AN:

250050

Hom.:

AF XY:

0.00735

AC XY:

994

AN XY:

135228

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00751

Gnomad ASJ exome

AF:

0.00480

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00536

Gnomad FIN exome

AF:

0.00428

Gnomad NFE exome

AF:

0.00968

Gnomad OTH exome

AF:

0.00951

GnomAD4 exome

AF:

0.00811

AC:

11853

AN:

1461558

Hom.:

Cov.:

AF XY:

0.00824

AC XY:

5993

AN XY:

727088

show subpopulations

Gnomad4 AFR exome

AF:

0.00114

Gnomad4 AMR exome

AF:

0.00754

Gnomad4 ASJ exome

AF:

0.00563

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00545

Gnomad4 FIN exome

AF:

0.00437

Gnomad4 NFE exome

AF:

0.00907

Gnomad4 OTH exome

AF:

0.00777

GnomAD4 genome

AF:

0.00645

AC:

982

AN:

152270

Hom.:

Cov.:

AF XY:

0.00643

AC XY:

479

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00164

Gnomad4 AMR

AF:

0.00935

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.00555

Gnomad4 NFE

AF:

0.00940

Gnomad4 OTH

AF:

0.00852

Alfa

AF:

0.00939

Hom.:

Bravo

AF:

0.00637

TwinsUK

AF:

0.00647

AC:

ALSPAC

AF:

0.0104

AC:

ESP6500AA

AF:

0.00182

AC:

ESP6500EA

AF:

0.00907

AC:

ExAC

AF:

0.00676

AC:

821

Asia WGS

AF:

0.00318

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

SLC45A3: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.8

DANN

Benign

0.82

DEOGEN2

Benign

0.015

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.056

LIST_S2

Benign

0.59

MetaRNN

Benign

0.0026

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.90

MutationTaster

Benign

1.0

PrimateAI

Benign

0.41

PROVEAN

Benign

0.11

REVEL

Benign

0.010

Sift

Benign

0.56

Sift4G

Benign

0.99

Polyphen

0.066

Vest4

0.068

MVP

0.014

MPC

0.30

ClinPred

0.0013

GERP RS

-1.4

Varity_R

0.027

gMVP

0.40

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