Variant rs3803927 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005071.3(SLC1A6):c.549-93A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 981,970 control chromosomes in the GnomAD database, including 23,399 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 2978 hom., cov: 31)

Exomes 𝑓: 0.21 ( 20421 hom. )

Consequence

SLC1A6
NM_005071.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.775

Variant links:

Genes affected

SLC1A6 (HGNC:10944): (solute carrier family 1 member 6) Predicted to enable high-affinity glutamate transmembrane transporter activity. Involved in neurotransmitter uptake. Located in intermediate filament cytoskeleton and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC1A6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A6	NM_005071.3 link	c.549-93A>G		intron_variant		ENST00000594383.2	NP_005062.1	P48664-1B7Z7Q5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A6	ENST00000594383.2 link	c.549-93A>G		intron_variant		2	NM_005071.3	ENSP00000472133.2		P48664-1M0R1V3

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28495

AN:

151970

Hom.:

2979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.275

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.177

GnomAD4 exome

AF:

0.214

AC:

177450

AN:

829880

Hom.:

20421

AF XY:

0.216

AC XY:

94163

AN XY:

436868

show subpopulations

Gnomad4 AFR exome

AF:

0.0995

Gnomad4 AMR exome

AF:

0.247

Gnomad4 ASJ exome

AF:

0.100

Gnomad4 EAS exome

AF:

0.240

Gnomad4 SAS exome

AF:

0.260

Gnomad4 FIN exome

AF:

0.269

Gnomad4 NFE exome

AF:

0.209

Gnomad4 OTH exome

AF:

0.204

GnomAD4 genome

AF:

0.187

AC:

28498

AN:

152090

Hom.:

2978

Cov.:

AF XY:

0.193

AC XY:

14359

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.228

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.266

Gnomad4 SAS

AF:

0.274

Gnomad4 FIN

AF:

0.265

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.178

Alfa

AF:

0.202

Hom.:

2708

Bravo

AF:

0.181

Asia WGS

AF:

0.290

AC:

1008

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

DANN

Benign

0.60

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over