dbSNP rs2011162: SLC6A14:c.*178C>A (chrX-116459133-C-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_007231.5(SLC6A14):c.*178C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., 0 hem., cov: 21)

Exomes 𝑓: 0.000040 ( 0 hom. 5 hem. )

Failed GnomAD Quality Control

Consequence

SLC6A14
NM_007231.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.231

Publications

16 publications found

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 Gene-Disease associations (from GenCC):

cystic fibrosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SLC6A14 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_007231.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BS2

High Hemizygotes in GnomAdExome4 at 5 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007231.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A14	NM_007231.5	MANE Select	c.*178C>A		3_prime_UTR	Exon 14 of 14	NP_009162.1	Q9UN76

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC6A14	ENST00000598581.3	TSL:1 MANE Select	c.*178C>A	3_prime_UTR	Exon 14 of 14	ENSP00000470801.1	Q9UN76
SLC6A14	ENST00000905559.1		c.*178C>A	3_prime_UTR	Exon 13 of 13	ENSP00000575618.1
SLC6A14	ENST00000961159.1		c.*178C>A	3_prime_UTR	Exon 13 of 13	ENSP00000631218.1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

108829

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000397

AC:

AN:

251614

Hom.:

Cov.:

AF XY:

0.0000704

AC XY:

AN XY:

71020

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6757

American (AMR)

AF:

0.00

AC:

AN:

8192

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

7993

East Asian (EAS)

AF:

0.000531

AC:

AN:

18818

South Asian (SAS)

AF:

0.00

AC:

AN:

9749

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24673

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1111

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

158532

Other (OTH)

AF:

0.00

AC:

AN:

15789

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

108829

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

31247

African (AFR)

AF:

0.00

AC:

AN:

30070

American (AMR)

AF:

0.00

AC:

AN:

10030

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2626

East Asian (EAS)

AF:

0.00

AC:

AN:

3427

South Asian (SAS)

AF:

0.00

AC:

AN:

2546

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5560

Middle Eastern (MID)

AF:

0.00

AC:

AN:

231

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

52202

Other (OTH)

AF:

0.00

AC:

AN:

1467

Alfa

AF:

0.00

Hom.:

3786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.89

(source)

DANN

Benign

0.34

PhyloP100

0.23

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over