Variant 1-110167097-T-C 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_001010898.4(SLC6A17):c.168T>C(p.Asp56Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 1,609,682 control chromosomes in the GnomAD database, including 213,991 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 18682 hom., cov: 24)

Exomes 𝑓: 0.51 ( 195309 hom. )

Consequence

SLC6A17
NM_001010898.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -5.63

Variant links:

Genes affected

SLC6A17 (HGNC:31399): (solute carrier family 6 member 17) The protein encoded by this gene is a member of the SLC6 family of transporters, which are responsible for the presynaptic uptake of most neurotransmitters. The encoded vesicular transporter is selective for proline, glycine, leucine and alanine. In mouse, the strongest expression of this gene was in cortical and hippocampal tissues where expression increased during embryonic brain development and peaked postnatally. Defects in this gene cause a form of autosomal recessive intellectual disability. [provided by RefSeq, Jul 2017]

SLC6A17 links:

SLC6A17-AS1 (HGNC:):

SLC6A17-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 1-110167097-T-C is Benign according to our data. Variant chr1-110167097-T-C is described in ClinVar as [Benign]. Clinvar id is 1333111.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-110167097-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-5.63 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A17	NM_001010898.4 linkuse as main transcript	c.168T>C	p.Asp56Asp	synonymous_variant	2/12	ENST00000331565.5	NP_001010898.1	Q9H1V8
SLC6A17-AS1	NR_183667.1 linkuse as main transcript	n.522A>G		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC6A17	ENST00000331565.5 linkuse as main transcript	c.168T>C	p.Asp56Asp	synonymous_variant	2/12	2	NM_001010898.4	ENSP00000330199.3	Q9H1V8
SLC6A17-AS1	ENST00000430098.2 linkuse as main transcript	n.522A>G		non_coding_transcript_exon_variant	2/3	1
SLC6A17-AS1	ENST00000418579.1 linkuse as main transcript	n.168A>G		non_coding_transcript_exon_variant	2/2	3
SLC6A17-AS1	ENST00000443008.1 linkuse as main transcript	n.507A>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.496

AC:

74104

AN:

149478

Hom.:

18666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.392

Gnomad ASJ

AF:

0.485

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.589

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.471

GnomAD3 exomes

AF:

0.451

AC:

111689

AN:

247750

Hom.:

26983

AF XY:

0.454

AC XY:

60761

AN XY:

133864

show subpopulations

Gnomad AFR exome

AF:

0.505

Gnomad AMR exome

AF:

0.263

Gnomad ASJ exome

AF:

0.486

Gnomad EAS exome

AF:

0.210

Gnomad SAS exome

AF:

0.364

Gnomad FIN exome

AF:

0.587

Gnomad NFE exome

AF:

0.532

Gnomad OTH exome

AF:

0.487

GnomAD4 exome

AF:

0.510

AC:

744414

AN:

1460088

Hom.:

195309

Cov.:

AF XY:

0.507

AC XY:

367963

AN XY:

726180

show subpopulations

Gnomad4 AFR exome

AF:

0.503

Gnomad4 AMR exome

AF:

0.276

Gnomad4 ASJ exome

AF:

0.491

Gnomad4 EAS exome

AF:

0.252

Gnomad4 SAS exome

AF:

0.360

Gnomad4 FIN exome

AF:

0.590

Gnomad4 NFE exome

AF:

0.537

Gnomad4 OTH exome

AF:

0.506

GnomAD4 genome

AF:

0.496

AC:

74153

AN:

149594

Hom.:

18682

Cov.:

AF XY:

0.491

AC XY:

35838

AN XY:

72920

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.392

Gnomad4 ASJ

AF:

0.485

Gnomad4 EAS

AF:

0.223

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.589

Gnomad4 NFE

AF:

0.534

Gnomad4 OTH

AF:

0.468

Alfa

AF:

0.502

Hom.:

7476

Bravo

AF:

0.482

Asia WGS

AF:

0.311

AC:

1084

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.086

DANN

Benign

0.62

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