Variant chr19-33210492-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_019849.3(SLC7A10):c.1238G>A(p.Arg413Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0096 in 1,603,636 control chromosomes in the GnomAD database, including 1,304 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.052 ( 689 hom., cov: 32)

Exomes 𝑓: 0.0052 ( 615 hom. )

Consequence

SLC7A10
NM_019849.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.63

Variant links:

Genes affected

SLC7A10 (HGNC:11058): (solute carrier family 7 member 10) SLC7A10, in association with 4F2HC (SLC3A2; MIM 158070), mediates high-affinity transport of D-serine and several other neutral amino acids (Nakauchi et al., 2000 [PubMed 10863037]).[supplied by OMIM, Mar 2008]

SLC7A10 links:

SLC7A10 (HGNC:):

SLC7A10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016815662).

BP6

Variant 19-33210492-C-T is Benign according to our data. Variant chr19-33210492-C-T is described in ClinVar as [Benign]. Clinvar id is 1286752.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A10	NM_019849.3 linkuse as main transcript	c.1238G>A	p.Arg413Gln	missense_variant	9/11	ENST00000253188.8	NP_062823.1	Q9NS82

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC7A10	ENST00000253188.8 linkuse as main transcript	c.1238G>A	p.Arg413Gln	missense_variant	9/11	1	NM_019849.3	ENSP00000253188.2	Q9NS82
SLC7A10	ENST00000590036.5 linkuse as main transcript	n.1141G>A		non_coding_transcript_exon_variant	8/10	5		ENSP00000465421.1	K7EK24
SLC7A10	ENST00000590490.1 linkuse as main transcript	n.1013G>A		non_coding_transcript_exon_variant	2/4	2

Frequencies

GnomAD3 genomes

AF:

0.0516

AC:

7846

AN:

152134

Hom.:

679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0158

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000309

Gnomad OTH

AF:

0.0310

GnomAD3 exomes

AF:

0.0130

AC:

3058

AN:

235368

Hom.:

233

AF XY:

0.00888

AC XY:

1140

AN XY:

128386

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.00730

Gnomad ASJ exome

AF:

0.000102

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000300

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000288

Gnomad OTH exome

AF:

0.00475

GnomAD4 exome

AF:

0.00518

AC:

7513

AN:

1451384

Hom.:

615

Cov.:

AF XY:

0.00433

AC XY:

3127

AN XY:

722012

show subpopulations

Gnomad4 AFR exome

AF:

0.189

Gnomad4 AMR exome

AF:

0.00792

Gnomad4 ASJ exome

AF:

0.0000768

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000396

Gnomad4 FIN exome

AF:

0.0000216

Gnomad4 NFE exome

AF:

0.000100

Gnomad4 OTH exome

AF:

0.0111

GnomAD4 genome

AF:

0.0518

AC:

7885

AN:

152252

Hom.:

689

Cov.:

AF XY:

0.0498

AC XY:

3710

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.182

Gnomad4 AMR

AF:

0.0156

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000309

Gnomad4 OTH

AF:

0.0307

Alfa

AF:

0.00868

Hom.:

Bravo

AF:

0.0581

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.179

AC:

789

ESP6500EA

AF:

0.000582

AC:

ExAC

AF:

0.0160

AC:

1946

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 06, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.27

CADD

Benign

DANN

Benign

0.72

DEOGEN2

Benign

0.30

Eigen

Benign

-0.35

Eigen_PC

Benign

-0.15

FATHMM_MKL

Benign

0.72

LIST_S2

Benign

0.52

MetaRNN

Benign

0.0017

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.70

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.28

REVEL

Benign

0.27

Sift

Benign

0.92

Sift4G

Benign

0.91

Polyphen

0.0090

Vest4

0.11

MPC

0.44

ClinPred

0.0061

GERP RS

4.9

Varity_R

0.13

gMVP

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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