Variant rs1766967 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001024845.3(SLC6A9):c.319+51C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 1,594,426 control chromosomes in the GnomAD database, including 7,547 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1409 hom., cov: 32)

Exomes 𝑓: 0.083 ( 6138 hom. )

Consequence

SLC6A9
NM_001024845.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.620

Variant links:

Genes affected

SLC6A9 (HGNC:11056): (solute carrier family 6 member 9) The amino acid glycine acts as an inhibitory neurotransmitter in the central nervous system. The protein encoded by this gene is one of two transporters that stop glycine signaling by removing it from the synaptic cleft. [provided by RefSeq, Jun 2016]

SLC6A9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 1-44009914-G-A is Benign according to our data. Variant chr1-44009914-G-A is described in ClinVar as [Benign]. Clinvar id is 1232090.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A9	NM_001024845.3 link	c.319+51C>T		intron_variant		ENST00000372310.8	NP_001020016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A9	ENST00000372310.8 link	c.319+51C>T		intron_variant		5	NM_001024845.3	ENSP00000361384.4		P48067-2

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18238

AN:

152092

Hom.:

1407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0726

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.0670

Gnomad OTH

AF:

0.116

GnomAD3 exomes

AF:

0.109

AC:

25989

AN:

239514

Hom.:

1708

AF XY:

0.104

AC XY:

13506

AN XY:

129380

show subpopulations

Gnomad AFR exome

AF:

0.209

Gnomad AMR exome

AF:

0.153

Gnomad ASJ exome

AF:

0.0737

Gnomad EAS exome

AF:

0.160

Gnomad SAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.118

Gnomad NFE exome

AF:

0.0714

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.0834

AC:

120224

AN:

1442214

Hom.:

6138

Cov.:

AF XY:

0.0833

AC XY:

59627

AN XY:

715996

show subpopulations

Gnomad4 AFR exome

AF:

0.212

Gnomad4 AMR exome

AF:

0.150

Gnomad4 ASJ exome

AF:

0.0729

Gnomad4 EAS exome

AF:

0.204

Gnomad4 SAS exome

AF:

0.115

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.0682

Gnomad4 OTH exome

AF:

0.0940

GnomAD4 genome

AF:

0.120

AC:

18256

AN:

152212

Hom.:

1409

Cov.:

AF XY:

0.121

AC XY:

9035

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.0726

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.0670

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.0759

Hom.:

971

Bravo

AF:

0.125

Asia WGS

AF:

0.129

AC:

448

AN:

3478

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 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.5

DANN

Benign

0.54

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