Variant X-70926625-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032803.6(SLC7A3):c.1522C>G(p.Leu508Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,191,787 control chromosomes in the GnomAD database, including 16,800 homozygotes. There are 57,771 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.26 ( 4487 hom., 8165 hem., cov: 22)

Exomes 𝑓: 0.14 ( 12313 hom. 49606 hem. )

Consequence

SLC7A3
NM_032803.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.420

Variant links:

Genes affected

SLC7A3 (HGNC:11061): (solute carrier family 7 member 3) This gene encodes a member of the solute carrier family 7. The encoded protein is a sodium-independent cationic amino acid transporter. Alternate splicing results in multiple transcripts that encoded the same protein.[provided by RefSeq, May 2010]

SLC7A3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=5.745551E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A3	NM_032803.6 linkuse as main transcript	c.1522C>G	p.Leu508Val	missense_variant	10/12	ENST00000374299.8	NP_116192.4	Q8WY07
SLC7A3	NM_001048164.3 linkuse as main transcript	c.1522C>G	p.Leu508Val	missense_variant	10/12		NP_001041629.1	Q8WY07
SLC7A3	XM_047442598.1 linkuse as main transcript	c.1522C>G	p.Leu508Val	missense_variant	9/11		XP_047298554.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A3	ENST00000374299.8 linkuse as main transcript	c.1522C>G	p.Leu508Val	missense_variant	10/12	1	NM_032803.6	ENSP00000363417.3		Q8WY07
SLC7A3	ENST00000298085.4 linkuse as main transcript	c.1522C>G	p.Leu508Val	missense_variant	10/12	2		ENSP00000298085.4		Q8WY07

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

28514

AN:

110244

Hom.:

4481

Cov.:

AF XY:

0.250

AC XY:

8126

AN XY:

32546

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.0221

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.0779

Gnomad MID

AF:

0.0928

Gnomad NFE

AF:

0.0877

Gnomad OTH

AF:

0.247

GnomAD3 exomes

AF:

0.238

AC:

36218

AN:

151911

Hom.:

5193

AF XY:

0.224

AC XY:

10369

AN XY:

46357

show subpopulations

Gnomad AFR exome

AF:

0.567

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.102

Gnomad EAS exome

AF:

0.465

Gnomad SAS exome

AF:

0.350

Gnomad FIN exome

AF:

0.0827

Gnomad NFE exome

AF:

0.0844

Gnomad OTH exome

AF:

0.180

GnomAD4 exome

AF:

0.137

AC:

148473

AN:

1081492

Hom.:

12313

Cov.:

AF XY:

0.141

AC XY:

49606

AN XY:

352210

show subpopulations

Gnomad4 AFR exome

AF:

0.572

Gnomad4 AMR exome

AF:

0.457

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.453

Gnomad4 SAS exome

AF:

0.342

Gnomad4 FIN exome

AF:

0.0854

Gnomad4 NFE exome

AF:

0.0888

Gnomad4 OTH exome

AF:

0.170

GnomAD4 genome

AF:

0.259

AC:

28567

AN:

110295

Hom.:

4487

Cov.:

AF XY:

0.250

AC XY:

8165

AN XY:

32609

show subpopulations

Gnomad4 AFR

AF:

0.555

Gnomad4 AMR

AF:

0.354

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.450

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.0779

Gnomad4 NFE

AF:

0.0877

Gnomad4 OTH

AF:

0.251

Alfa

AF:

0.131

Hom.:

3702

Bravo

AF:

0.301

TwinsUK

AF:

0.0974

AC:

361

ALSPAC

AF:

0.0921

AC:

266

ESP6500AA

AF:

0.565

AC:

2165

ESP6500EA

AF:

0.0949

AC:

638

ExAC

AF:

0.216

AC:

25798

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.058

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.62

DANN

Benign

0.16

DEOGEN2

Benign

0.018

T;T

FATHMM_MKL

Benign

0.0080

LIST_S2

Benign

0.071

.;T

MetaRNN

Benign

0.000057

T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-2.3

N;N

PrimateAI

Benign

0.38

PROVEAN

Benign

1.1

N;N

REVEL

Benign

0.21

Sift

Benign

0.58

T;T

Sift4G

Benign

0.62

T;T

Polyphen

0.0

B;B

Vest4

0.016

MPC

0.33

ClinPred

0.0012

GERP RS

4.2

Varity_R

0.055

gMVP

0.24

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over