Genetic Variant SLC6A14:p.Ser358Ser (chrX-116451585-C-T) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_007231.5(SLC6A14):c.1074C>T(p.Ser358Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00527 in 1,207,619 control chromosomes in the GnomAD database, including 15 homozygotes. There are 2,068 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0042 ( 4 hom., 129 hem., cov: 23)

Exomes 𝑓: 0.0054 ( 11 hom. 1939 hem. )

Consequence

SLC6A14
NM_007231.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.430

Variant links:

Genes affected

SLC6A14 (HGNC:11047): (solute carrier family 6 member 14) This gene encodes a member of the solute carrier family 6. Members of this family are sodium and chloride dependent neurotransmitter transporters. The encoded protein transports both neutral and cationic amino acids. This protein may also function as a beta-alanine carrier. Mutations in this gene may be associated with X-linked obesity. A pseudogene of this gene is found on chromosome X.[provided by RefSeq, May 2010]

SLC6A14 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP6

Variant X-116451585-C-T is Benign according to our data. Variant chrX-116451585-C-T is described in ClinVar as [Benign]. Clinvar id is 788934.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.43 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A14	NM_007231.5 link	c.1074C>T	p.Ser358Ser	synonymous_variant	Exon 8 of 14	ENST00000598581.3	NP_009162.1	Q9UN76B2R8J1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A14	ENST00000598581.3 link	c.1074C>T	p.Ser358Ser	synonymous_variant	Exon 8 of 14	1	NM_007231.5	ENSP00000470801.1		Q9UN76

Frequencies

GnomAD3 genomes

AF:

0.00419

AC:

465

AN:

110856

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000754

Gnomad AMI

AF:

0.0706

Gnomad AMR

AF:

0.00281

Gnomad ASJ

AF:

0.000379

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00302

Gnomad FIN

AF:

0.0124

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00531

Gnomad OTH

AF:

0.00201

GnomAD2 exomes

AF:

0.00464

AC:

849

AN:

182943

AF XY:

0.00488

show subpopulations

Gnomad AFR exome

AF:

0.000836

Gnomad AMR exome

AF:

0.00336

Gnomad ASJ exome

AF:

0.00201

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0121

Gnomad NFE exome

AF:

0.00544

Gnomad OTH exome

AF:

0.00730

GnomAD4 exome

AF:

0.00538

AC:

5898

AN:

1096718

Hom.:

Cov.:

AF XY:

0.00535

AC XY:

1939

AN XY:

362168

show subpopulations

Gnomad4 AFR exome

AF:

0.000986

AC:

AN:

26376

Gnomad4 AMR exome

AF:

0.00315

AC:

111

AN:

35188

Gnomad4 ASJ exome

AF:

0.00181

AC:

AN:

19370

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

30175

Gnomad4 SAS exome

AF:

0.00394

AC:

213

AN:

54092

Gnomad4 FIN exome

AF:

0.0130

AC:

526

AN:

40514

Gnomad4 NFE exome

AF:

0.00564

AC:

4741

AN:

840837

Gnomad4 Remaining exome

AF:

0.00519

AC:

239

AN:

46039

Heterozygous variant carriers

202

403

605

806

1008

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

174

348

522

696

870

<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:

0.00420

AC:

466

AN:

110901

Hom.:

Cov.:

AF XY:

0.00389

AC XY:

129

AN XY:

33135

show subpopulations

Gnomad4 AFR

AF:

0.000752

AC:

0.000752273

AN:

0.000752273

Gnomad4 AMR

AF:

0.00290

AC:

0.00289995

AN:

0.00289995

Gnomad4 ASJ

AF:

0.000379

AC:

0.000378501

AN:

0.000378501

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00303

AC:

0.00303145

AN:

0.00303145

Gnomad4 FIN

AF:

0.0124

AC:

0.0123775

AN:

0.0123775

Gnomad4 NFE

AF:

0.00531

AC:

0.00530669

AN:

0.00530669

Gnomad4 OTH

AF:

0.00199

AC:

0.00198544

AN:

0.00198544

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

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:

0.00458

Hom.:

Bravo

AF:

0.00354

EpiCase

AF:

0.00493

EpiControl

AF:

0.00457

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jul 06, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

6.3

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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