Variant 19-33209375-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_019849.3(SLC7A10):c.1374G>T(p.Thr458Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 1,613,918 control chromosomes in the GnomAD database, including 2,417 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 205 hom., cov: 32)

Exomes 𝑓: 0.051 ( 2212 hom. )

Consequence

SLC7A10
NM_019849.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.40

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 19-33209375-C-A is Benign according to our data. Variant chr19-33209375-C-A is described in ClinVar as [Benign]. Clinvar id is 1224054.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.4 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A10	NM_019849.3 link	c.1374G>T	p.Thr458Thr	synonymous_variant	10/11	ENST00000253188.8	NP_062823.1	Q9NS82

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC7A10	ENST00000253188.8 link	c.1374G>T	p.Thr458Thr	synonymous_variant	10/11	1	NM_019849.3	ENSP00000253188.2	Q9NS82
SLC7A10	ENST00000590036.5 link	n.*107G>T		non_coding_transcript_exon_variant	9/10	5		ENSP00000465421.1	K7EK24
SLC7A10	ENST00000590490.1 link	n.1149G>T		non_coding_transcript_exon_variant	3/4	2
SLC7A10	ENST00000590036.5 link	n.*107G>T		3_prime_UTR_variant	9/10	5		ENSP00000465421.1	K7EK24

Frequencies

GnomAD3 genomes

AF:

0.0453

AC:

6884

AN:

152020

Hom.:

202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0192

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0742

Gnomad ASJ

AF:

0.0479

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.0272

Gnomad FIN

AF:

0.0340

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0513

Gnomad OTH

AF:

0.0465

GnomAD3 exomes

AF:

0.0563

AC:

14161

AN:

251386

Hom.:

493

AF XY:

0.0538

AC XY:

7307

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.0171

Gnomad AMR exome

AF:

0.0916

Gnomad ASJ exome

AF:

0.0442

Gnomad EAS exome

AF:

0.130

Gnomad SAS exome

AF:

0.0256

Gnomad FIN exome

AF:

0.0376

Gnomad NFE exome

AF:

0.0522

Gnomad OTH exome

AF:

0.0572

GnomAD4 exome

AF:

0.0508

AC:

74217

AN:

1461780

Hom.:

2212

Cov.:

AF XY:

0.0499

AC XY:

36276

AN XY:

727188

show subpopulations

Gnomad4 AFR exome

AF:

0.0176

Gnomad4 AMR exome

AF:

0.0898

Gnomad4 ASJ exome

AF:

0.0440

Gnomad4 EAS exome

AF:

0.133

Gnomad4 SAS exome

AF:

0.0251

Gnomad4 FIN exome

AF:

0.0405

Gnomad4 NFE exome

AF:

0.0500

Gnomad4 OTH exome

AF:

0.0485

GnomAD4 genome

AF:

0.0453

AC:

6898

AN:

152138

Hom.:

205

Cov.:

AF XY:

0.0455

AC XY:

3382

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0193

Gnomad4 AMR

AF:

0.0748

Gnomad4 ASJ

AF:

0.0479

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.0274

Gnomad4 FIN

AF:

0.0340

Gnomad4 NFE

AF:

0.0513

Gnomad4 OTH

AF:

0.0461

Alfa

AF:

0.0353

Hom.:

Bravo

AF:

0.0487

Asia WGS

AF:

0.0680

AC:

235

AN:

3478

EpiCase

AF:

0.0503

EpiControl

AF:

0.0514

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 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.16

DANN

Benign

0.78

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