Variant 9-4561421-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004170.6(SLC1A1):c.233-28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,348,496 control chromosomes in the GnomAD database, including 16,507 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1663 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14844 hom. )

Consequence

SLC1A1
NM_004170.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.127

Variant links:

Genes affected

SLC1A1 (HGNC:10939): (solute carrier family 1 member 1) This gene encodes a member of the high-affinity glutamate transporters that play an essential role in transporting glutamate across plasma membranes. In brain, these transporters are crucial in terminating the postsynaptic action of the neurotransmitter glutamate, and in maintaining extracellular glutamate concentrations below neurotoxic levels. This transporter also transports aspartate, and mutations in this gene are thought to cause dicarboxylicamino aciduria, also known as glutamate-aspartate transport defect. [provided by RefSeq, Mar 2010]

SLC1A1 links:

SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]

SPATA6L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 9-4561421-T-C is Benign according to our data. Variant chr9-4561421-T-C is described in ClinVar as [Benign]. Clinvar id is 1291041.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A1	NM_004170.6 linkuse as main transcript	c.233-28T>C		intron_variant		ENST00000262352.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
SLC1A1	ENST00000262352.8 linkuse as main transcript	c.233-28T>C	intron_variant	1	NM_004170.6	P1
SPATA6L	ENST00000485616.5 linkuse as main transcript	c.*782-7033A>G	intron_variant, NMD_transcript_variant	2
SLC1A1	ENST00000490167.1 linkuse as main transcript	n.277-28T>C	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17992

AN:

152082

Hom.:

1657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0259

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.101

GnomAD3 exomes

AF:

0.166

AC:

41599

AN:

251222

Hom.:

4990

AF XY:

0.158

AC XY:

21393

AN XY:

135782

show subpopulations

Gnomad AFR exome

AF:

0.0244

Gnomad AMR exome

AF:

0.277

Gnomad ASJ exome

AF:

0.0442

Gnomad EAS exome

AF:

0.443

Gnomad SAS exome

AF:

0.118

Gnomad FIN exome

AF:

0.221

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.141

AC:

168884

AN:

1196296

Hom.:

14844

Cov.:

AF XY:

0.139

AC XY:

84442

AN XY:

608702

show subpopulations

Gnomad4 AFR exome

AF:

0.0207

Gnomad4 AMR exome

AF:

0.266

Gnomad4 ASJ exome

AF:

0.0479

Gnomad4 EAS exome

AF:

0.418

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.217

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.129

GnomAD4 genome

AF:

0.118

AC:

17998

AN:

152200

Hom.:

1663

Cov.:

AF XY:

0.125

AC XY:

9296

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.0258

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.0455

Gnomad4 EAS

AF:

0.426

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.124

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.110

Hom.:

198

Bravo

AF:

0.115

Asia WGS

AF:

0.244

AC:

848

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.4

DANN

Benign

0.40

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