Variant chr1-43997498-G-A 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.*47C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 1,549,872 control chromosomes in the GnomAD database, including 7,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1595 hom., cov: 32)

Exomes 𝑓: 0.083 ( 5899 hom. )

Consequence

SLC6A9
NM_001024845.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.801

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=-0.75).

BP6

Variant 1-43997498-G-A is Benign according to our data. Variant chr1-43997498-G-A is described in ClinVar as [Benign]. Clinvar id is 1242659.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A9	NM_001024845.3 linkuse as main transcript	c.*47C>T		3_prime_UTR_variant	14/14	ENST00000372310.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A9	ENST00000372310.8 linkuse as main transcript	c.*47C>T		3_prime_UTR_variant	14/14	5	NM_001024845.3	P1	P48067-2

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18940

AN:

152032

Hom.:

1591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.0718

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.0960

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.0661

Gnomad OTH

AF:

0.118

GnomAD3 exomes

AF:

0.106

AC:

25091

AN:

237020

Hom.:

1650

AF XY:

0.102

AC XY:

13199

AN XY:

129990

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.148

Gnomad ASJ exome

AF:

0.0713

Gnomad EAS exome

AF:

0.143

Gnomad SAS exome

AF:

0.106

Gnomad FIN exome

AF:

0.116

Gnomad NFE exome

AF:

0.0708

Gnomad OTH exome

AF:

0.104

GnomAD4 exome

AF:

0.0825

AC:

115329

AN:

1397720

Hom.:

5899

Cov.:

AF XY:

0.0822

AC XY:

57420

AN XY:

698510

show subpopulations

Gnomad4 AFR exome

AF:

0.238

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.0714

Gnomad4 EAS exome

AF:

0.188

Gnomad4 SAS exome

AF:

0.108

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.0673

Gnomad4 OTH exome

AF:

0.0933

GnomAD4 genome

AF:

0.125

AC:

18965

AN:

152152

Hom.:

1595

Cov.:

AF XY:

0.126

AC XY:

9381

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.120

Gnomad4 ASJ

AF:

0.0718

Gnomad4 EAS

AF:

0.151

Gnomad4 SAS

AF:

0.0965

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.0661

Gnomad4 OTH

AF:

0.116

Alfa

AF:

0.0934

Hom.:

238

Bravo

AF:

0.130

Asia WGS

AF:

0.119

AC:

413

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

-0.75

CADD

Benign

DANN

Benign

0.77

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