11-20601059-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004211.5(SLC6A5):c.4-70A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 1,479,216 control chromosomes in the GnomAD database, including 8,076 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 1025 hom., cov: 33)
Exomes 𝑓: 0.099 ( 7051 hom. )
Consequence
SLC6A5
NM_004211.5 intron
NM_004211.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.18
Publications
1 publications found
Genes affected
SLC6A5 (HGNC:11051): (solute carrier family 6 member 5) This gene encodes a sodium- and chloride-dependent glycine neurotransmitter transporter. This integral membrane glycoprotein is responsible for the clearance of extracellular glycine during glycine-mediated neurotransmission. This protein is found in glycinergic axons and maintains a high presynaptic pool of neurotransmitter at glycinergic synapses. Mutations in this gene cause hyperekplexia; a heterogenous neurological disorder characterized by exaggerated startle responses and neonatal apnea. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
SLC6A5 Gene-Disease associations (from GenCC):
- hyperekplexia 3Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- hereditary hyperekplexiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 11-20601059-A-G is Benign according to our data. Variant chr11-20601059-A-G is described in ClinVar as Benign. ClinVar VariationId is 1297945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.111 AC: 16849AN: 152154Hom.: 1023 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
16849
AN:
152154
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0991 AC: 131442AN: 1326944Hom.: 7051 AF XY: 0.0982 AC XY: 64473AN XY: 656478 show subpopulations
GnomAD4 exome
AF:
AC:
131442
AN:
1326944
Hom.:
AF XY:
AC XY:
64473
AN XY:
656478
show subpopulations
African (AFR)
AF:
AC:
4916
AN:
29276
American (AMR)
AF:
AC:
2001
AN:
29152
Ashkenazi Jewish (ASJ)
AF:
AC:
3501
AN:
23434
East Asian (EAS)
AF:
AC:
77
AN:
35742
South Asian (SAS)
AF:
AC:
4410
AN:
74072
European-Finnish (FIN)
AF:
AC:
1961
AN:
34056
Middle Eastern (MID)
AF:
AC:
534
AN:
5474
European-Non Finnish (NFE)
AF:
AC:
108314
AN:
1040042
Other (OTH)
AF:
AC:
5728
AN:
55696
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
5935
11870
17804
23739
29674
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4046
8092
12138
16184
20230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.111 AC: 16857AN: 152272Hom.: 1025 Cov.: 33 AF XY: 0.106 AC XY: 7871AN XY: 74462 show subpopulations
GnomAD4 genome
AF:
AC:
16857
AN:
152272
Hom.:
Cov.:
33
AF XY:
AC XY:
7871
AN XY:
74462
show subpopulations
African (AFR)
AF:
AC:
6796
AN:
41540
American (AMR)
AF:
AC:
1336
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
480
AN:
3472
East Asian (EAS)
AF:
AC:
36
AN:
5186
South Asian (SAS)
AF:
AC:
307
AN:
4834
European-Finnish (FIN)
AF:
AC:
543
AN:
10616
Middle Eastern (MID)
AF:
AC:
34
AN:
294
European-Non Finnish (NFE)
AF:
AC:
7049
AN:
68006
Other (OTH)
AF:
AC:
200
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
767
1533
2300
3066
3833
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
176
352
528
704
880
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
189
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
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
May 17, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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