Variant 1-53092598-A-G 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_006671.6(SLC1A7):c.987T>C(p.Arg329=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 1,613,898 control chromosomes in the GnomAD database, including 574,969 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.82 ( 51981 hom., cov: 33)

Exomes 𝑓: 0.85 ( 522988 hom. )

Consequence

SLC1A7
NM_006671.6 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.51

Variant links:

Genes affected

SLC1A7 (HGNC:10945): (solute carrier family 1 member 7) Predicted to enable anion transmembrane transporter activity. Involved in neurotransmitter reuptake. Predicted to be located in plasma membrane. Predicted to be active in glutamatergic synapse. Predicted to be integral component of postsynaptic membrane and integral component of presynaptic membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC1A7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 1-53092598-A-G is Benign according to our data. Variant chr1-53092598-A-G is described in ClinVar as [Benign]. Clinvar id is 1235045.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A7	NM_006671.6 linkuse as main transcript	c.987T>C	p.Arg329=	synonymous_variant	7/11	ENST00000371494.9	NP_006662.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A7	ENST00000371494.9 linkuse as main transcript	c.987T>C	p.Arg329=	synonymous_variant	7/11	1	NM_006671.6	ENSP00000360549	P1	O00341-1

Frequencies

GnomAD3 genomes

AF:

0.824

AC:

125337

AN:

152062

Hom.:

51934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.752

Gnomad AMI

AF:

0.854

Gnomad AMR

AF:

0.888

Gnomad ASJ

AF:

0.804

Gnomad EAS

AF:

0.951

Gnomad SAS

AF:

0.830

Gnomad FIN

AF:

0.882

Gnomad MID

AF:

0.807

Gnomad NFE

AF:

0.835

Gnomad OTH

AF:

0.832

GnomAD3 exomes

AF:

0.849

AC:

213240

AN:

251248

Hom.:

90907

AF XY:

0.844

AC XY:

114694

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.751

Gnomad AMR exome

AF:

0.926

Gnomad ASJ exome

AF:

0.805

Gnomad EAS exome

AF:

0.956

Gnomad SAS exome

AF:

0.824

Gnomad FIN exome

AF:

0.868

Gnomad NFE exome

AF:

0.829

Gnomad OTH exome

AF:

0.843

GnomAD4 exome

AF:

0.845

AC:

1235321

AN:

1461718

Hom.:

522988

Cov.:

AF XY:

0.844

AC XY:

613577

AN XY:

727182

show subpopulations

Gnomad4 AFR exome

AF:

0.747

Gnomad4 AMR exome

AF:

0.921

Gnomad4 ASJ exome

AF:

0.804

Gnomad4 EAS exome

AF:

0.960

Gnomad4 SAS exome

AF:

0.825

Gnomad4 FIN exome

AF:

0.864

Gnomad4 NFE exome

AF:

0.843

Gnomad4 OTH exome

AF:

0.842

GnomAD4 genome

AF:

0.824

AC:

125442

AN:

152180

Hom.:

51981

Cov.:

AF XY:

0.829

AC XY:

61659

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.752

Gnomad4 AMR

AF:

0.888

Gnomad4 ASJ

AF:

0.804

Gnomad4 EAS

AF:

0.951

Gnomad4 SAS

AF:

0.830

Gnomad4 FIN

AF:

0.882

Gnomad4 NFE

AF:

0.835

Gnomad4 OTH

AF:

0.833

Alfa

AF:

0.831

Hom.:

56433

Bravo

AF:

0.823

Asia WGS

AF:

0.894

AC:

3108

AN:

3478

EpiCase

AF:

0.827

EpiControl

AF:

0.827

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	Jul 18, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.042

DANN

Benign

0.67

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