Variant 17-81246137-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001037984.3(SLC38A10):c.2779A>G(p.Lys927Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00398 in 1,610,394 control chromosomes in the GnomAD database, including 22 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 (no stars).

Frequency

Genomes: 𝑓 0.0030 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0041 ( 21 hom. )

Consequence

SLC38A10
NM_001037984.3 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.153

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:

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=0.004170418).

BP6

Variant 17-81246137-T-C is Benign according to our data. Variant chr17-81246137-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3037674.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 21 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC38A10	NM_001037984.3 link	c.2779A>G	p.Lys927Glu	missense_variant	16/16	ENST00000374759.8	NP_001033073.1	Q9HBR0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC38A10	ENST00000374759.8 link	c.2779A>G	p.Lys927Glu	missense_variant	16/16	5	NM_001037984.3	ENSP00000363891.3	Q9HBR0-1
SLC38A10	ENST00000539643.1 link	n.855A>G		non_coding_transcript_exon_variant	2/2	1
SLC38A10	ENST00000540966.5 link	c.*41A>G		downstream_gene_variant		3		ENSP00000437601.1	H0YF92

Frequencies

GnomAD3 genomes

AF:

0.00296

AC:

451

AN:

152230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000651

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00339

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00501

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00287

AC:

705

AN:

245812

Hom.:

AF XY:

0.00303

AC XY:

407

AN XY:

134234

show subpopulations

Gnomad AFR exome

AF:

0.000131

Gnomad AMR exome

AF:

0.000697

Gnomad ASJ exome

AF:

0.00453

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000720

Gnomad FIN exome

AF:

0.00353

Gnomad NFE exome

AF:

0.00472

Gnomad OTH exome

AF:

0.00234

GnomAD4 exome

AF:

0.00408

AC:

5956

AN:

1458046

Hom.:

Cov.:

AF XY:

0.00411

AC XY:

2985

AN XY:

725446

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.000896

Gnomad4 ASJ exome

AF:

0.00475

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000603

Gnomad4 FIN exome

AF:

0.00350

Gnomad4 NFE exome

AF:

0.00478

Gnomad4 OTH exome

AF:

0.00386

GnomAD4 genome

AF:

0.00296

AC:

451

AN:

152348

Hom.:

Cov.:

AF XY:

0.00293

AC XY:

218

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.000649

Gnomad4 AMR

AF:

0.00118

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00339

Gnomad4 NFE

AF:

0.00501

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00411

Hom.:

Bravo

AF:

0.00273

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00389

AC:

ESP6500AA

AF:

0.000244

AC:

ESP6500EA

AF:

0.00538

AC:

ExAC

AF:

0.00281

AC:

339

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00436

EpiControl

AF:

0.00409

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

May 22, 2020

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

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.1

DANN

Benign

0.37

DEOGEN2

Benign

0.019

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.061

LIST_S2

Benign

0.35

M_CAP

Benign

0.0024

MetaRNN

Benign

0.0042

MetaSVM

Benign

-0.96

MutationAssessor

Benign

1.2

PrimateAI

Benign

0.40

PROVEAN

Benign

-1.3

REVEL

Benign

0.13

Sift

Benign

0.45

Sift4G

Benign

0.19

Polyphen

0.0

Vest4

0.094

MVP

0.040

MPC

0.16

ClinPred

0.0027

GERP RS

-4.5

Varity_R

0.14

gMVP

0.18

Splicing

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