Variant chr17-81251240-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_138570.4(SLC38A10):c.2318G>A(p.Arg773His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00256 in 1,454,316 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0021 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0026 ( 7 hom. )

Consequence

SLC38A10
NM_138570.4 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.357

Variant links:

Genes affected

SLC38A10 (HGNC:28237): (solute carrier family 38 member 10) Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport. Predicted to act upstream of or within bone development. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

SLC38A10 links:

ENSG00000276101 (HGNC:):

ENSG00000276101 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024465024).

BP6

Variant 17-81251240-C-T is Benign according to our data. Variant chr17-81251240-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3050225.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC38A10	NM_001037984.3 link	c.2065+253G>A		intron_variant		ENST00000374759.8	NP_001033073.1	Q9HBR0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC38A10	ENST00000374759.8 link	c.2065+253G>A		intron_variant		5	NM_001037984.3	ENSP00000363891.3		Q9HBR0-1

Frequencies

GnomAD3 genomes

AF:

0.00206

AC:

262

AN:

127188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00113

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00147

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00108

Gnomad FIN

AF:

0.00380

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00266

Gnomad OTH

AF:

0.00167

GnomAD3 exomes

AF:

0.00180

AC:

417

AN:

231572

Hom.:

AF XY:

0.00173

AC XY:

218

AN XY:

125656

show subpopulations

Gnomad AFR exome

AF:

0.000651

Gnomad AMR exome

AF:

0.000422

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00139

Gnomad FIN exome

AF:

0.00423

Gnomad NFE exome

AF:

0.00244

Gnomad OTH exome

AF:

0.00159

GnomAD4 exome

AF:

0.00260

AC:

3456

AN:

1327066

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

1709

AN XY:

658924

show subpopulations

Gnomad4 AFR exome

AF:

0.000793

Gnomad4 AMR exome

AF:

0.000446

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000509

Gnomad4 SAS exome

AF:

0.00167

Gnomad4 FIN exome

AF:

0.00511

Gnomad4 NFE exome

AF:

0.00286

Gnomad4 OTH exome

AF:

0.00211

GnomAD4 genome

AF:

0.00206

AC:

262

AN:

127250

Hom.:

Cov.:

AF XY:

0.00195

AC XY:

122

AN XY:

62496

show subpopulations

Gnomad4 AFR

AF:

0.00112

Gnomad4 AMR

AF:

0.00147

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00108

Gnomad4 FIN

AF:

0.00380

Gnomad4 NFE

AF:

0.00266

Gnomad4 OTH

AF:

0.00165

Alfa

AF:

0.00167

Hom.:

ESP6500AA

AF:

0.0141

AC:

ESP6500EA

AF:

0.00244

AC:

ExAC

AF:

0.00188

AC:

210

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC38A10-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 12, 2022

This variant is classified as likely 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

-0.80

CADD

Benign

0.14

DANN

Benign

0.29

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0024

MetaSVM

Benign

-0.99

PROVEAN

Benign

-0.42

REVEL

Benign

0.035

Sift

Pathogenic

0.0

Sift4G

Benign

0.55

Polyphen

0.034

Vest4

0.14

MVP

0.072

ClinPred

0.0069

GERP RS

-0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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