Genetic Variant ENST00000288439.9:c.2318G>A (chr17-81251240-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The ENST00000288439.9(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. 13/17 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
ENST00000288439.9 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.357

Publications

2 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 3050225.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000288439.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A10	NM_001037984.3	MANE Select	c.2065+253G>A		intron	N/A	NP_001033073.1	Q9HBR0-1
	SLC38A10	NM_138570.4		c.2318G>A	p.Arg773His	missense	Exon 14 of 14	NP_612637.1	Q9HBR0-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC38A10	ENST00000288439.9	TSL:1	c.2318G>A	p.Arg773His	missense	Exon 14 of 14	ENSP00000288439.5	Q9HBR0-2
SLC38A10	ENST00000374759.8	TSL:5 MANE Select	c.2065+253G>A		intron	N/A	ENSP00000363891.3	Q9HBR0-1
SLC38A10	ENST00000947966.1		c.2065+253G>A		intron	N/A	ENSP00000618025.1

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

GnomAD2 exomes

AF:

0.00180

AC:

417

AN:

231572

AF XY:

0.00173

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 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

African (AFR)

AF:

0.000793

AC:

AN:

18906

American (AMR)

AF:

0.000446

AC:

AN:

38130

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21262

East Asian (EAS)

AF:

0.0000509

AC:

AN:

39328

South Asian (SAS)

AF:

0.00167

AC:

135

AN:

80740

European-Finnish (FIN)

AF:

0.00511

AC:

259

AN:

50682

Middle Eastern (MID)

AF:

0.000630

AC:

AN:

4760

European-Non Finnish (NFE)

AF:

0.00286

AC:

2912

AN:

1019796

Other (OTH)

AF:

0.00211

AC:

113

AN:

53462

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

209

419

628

838

1047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00206

AC:

262

AN:

127250

Hom.:

Cov.:

AF XY:

0.00195

AC XY:

122

AN XY:

62496

show subpopulations

African (AFR)

AF:

0.00112

AC:

AN:

24898

American (AMR)

AF:

0.00147

AC:

AN:

13618

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2900

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00108

AC:

AN:

4618

European-Finnish (FIN)

AF:

0.00380

AC:

AN:

10274

Middle Eastern (MID)

AF:

0.00

AC:

AN:

252

European-Non Finnish (NFE)

AF:

0.00266

AC:

167

AN:

62846

Other (OTH)

AF:

0.00165

AC:

AN:

1816

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00175

Hom.:

ESP6500AA

AF:

0.0141

AC:

ESP6500EA

AF:

0.00244

AC:

ExAC

AF:

0.00188

AC:

210

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

SLC38A10-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.14

(source)

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

PhyloP100

-0.36

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

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over