chr3-11015683-G-A

Variant summary

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

The NM_003042.4(SLC6A1):​c.-204G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,160 control chromosomes in the GnomAD database, including 17,991 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17973 hom., cov: 33)
Exomes 𝑓: 0.57 ( 18 hom. )

Consequence

SLC6A1
NM_003042.4 5_prime_UTR

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 0.451
Variant links:
Genes affected
SLC6A1 (HGNC:11042): (solute carrier family 6 member 1) The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]
SLC6A1-AS1 (HGNC:40546): (SLC6A1 antisense RNA 1)

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=-0.82).
BP6
Variant 3-11015683-G-A is Benign according to our data. Variant chr3-11015683-G-A is described in ClinVar as [Benign]. Clinvar id is 1246526.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC6A1NM_003042.4 linkuse as main transcriptc.-204G>A 5_prime_UTR_variant 2/16 ENST00000287766.10
SLC6A1-AS1NR_046647.1 linkuse as main transcriptn.105+3437C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC6A1ENST00000287766.10 linkuse as main transcriptc.-204G>A 5_prime_UTR_variant 2/161 NM_003042.4 P1
SLC6A1-AS1ENST00000414969.2 linkuse as main transcriptn.105+3437C>T intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.468
AC:
71136
AN:
151920
Hom.:
17960
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.279
Gnomad AMI
AF:
0.505
Gnomad AMR
AF:
0.577
Gnomad ASJ
AF:
0.446
Gnomad EAS
AF:
0.396
Gnomad SAS
AF:
0.388
Gnomad FIN
AF:
0.594
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.551
Gnomad OTH
AF:
0.472
GnomAD4 exome
AF:
0.566
AC:
69
AN:
122
Hom.:
18
Cov.:
0
AF XY:
0.598
AC XY:
49
AN XY:
82
show subpopulations
Gnomad4 FIN exome
AF:
0.538
Gnomad4 NFE exome
AF:
0.525
Gnomad4 OTH exome
AF:
0.813
GnomAD4 genome
AF:
0.468
AC:
71177
AN:
152038
Hom.:
17973
Cov.:
33
AF XY:
0.469
AC XY:
34828
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.279
Gnomad4 AMR
AF:
0.577
Gnomad4 ASJ
AF:
0.446
Gnomad4 EAS
AF:
0.397
Gnomad4 SAS
AF:
0.386
Gnomad4 FIN
AF:
0.594
Gnomad4 NFE
AF:
0.551
Gnomad4 OTH
AF:
0.478
Alfa
AF:
0.486
Hom.:
2787
Bravo
AF:
0.459
Asia WGS
AF:
0.402
AC:
1400
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxDec 19, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
6.0
DANN
Benign
0.79

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.

Other links and lift over

dbSNP: rs6342; hg19: chr3-11057369; API