chr11-68684965-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_015973.5(GAL):c.42C>T(p.Leu14Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,457,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
GAL
NM_015973.5 synonymous
NM_015973.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.922
Publications
0 publications found
Genes affected
GAL (HGNC:4114): (galanin and GMAP prepropeptide) This gene encodes a neuroendocrine peptide that is widely expressed in the central and peripheral nervous systems and also the gastrointestinal tract, pancreas, adrenal gland and urogenital tract. The encoded protein is a precursor that is proteolytically processed to generate two mature peptides: galanin and galanin message-associated peptide (GMAP). Galanin has diverse physiological functions including nociception, feeding and energy homeostasis, osmotic regulation and water balance. GMAP has been demonstrated to possess antifungal activity and hypothesized to be part of the innate immune system. [provided by RefSeq, Jul 2015]
GAL Gene-Disease associations (from GenCC):
- familial temporal lobe epilepsy 8Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 11-68684965-C-T is Benign according to our data. Variant chr11-68684965-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1146014.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.922 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_015973.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GAL | TSL:1 MANE Select | c.42C>T | p.Leu14Leu | synonymous | Exon 2 of 6 | ENSP00000265643.3 | P22466 | ||
| GAL | c.42C>T | p.Leu14Leu | synonymous | Exon 2 of 7 | ENSP00000603516.1 | ||||
| GAL | c.42C>T | p.Leu14Leu | synonymous | Exon 2 of 6 | ENSP00000603515.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1457174Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 724762 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1457174
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
724762
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33386
American (AMR)
AF:
AC:
1
AN:
44502
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25978
East Asian (EAS)
AF:
AC:
0
AN:
39606
South Asian (SAS)
AF:
AC:
0
AN:
85538
European-Finnish (FIN)
AF:
AC:
0
AN:
52090
Middle Eastern (MID)
AF:
AC:
0
AN:
5644
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1110324
Other (OTH)
AF:
AC:
0
AN:
60106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Familial temporal lobe epilepsy 8 (1)
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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