rs542684427
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015973.5(GAL):c.66G>A(p.Ala22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000275 in 1,602,084 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: 𝑓 0.00016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
GAL
NM_015973.5 synonymous
NM_015973.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.175
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
Variant 11-68684989-G-A is Benign according to our data. Variant chr11-68684989-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 475917.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.175 with no splicing effect.
BS2
?
High AC in GnomAd4 at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAL | NM_015973.5 | c.66G>A | p.Ala22= | synonymous_variant | 2/6 | ENST00000265643.4 | |
LOC107984343 | XR_001748281.1 | n.230+2852C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAL | ENST00000265643.4 | c.66G>A | p.Ala22= | synonymous_variant | 2/6 | 1 | NM_015973.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152222Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000363 AC: 8AN: 220340Hom.: 0 AF XY: 0.0000166 AC XY: 2AN XY: 120566
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GnomAD4 exome AF: 0.0000138 AC: 20AN: 1449744Hom.: 0 Cov.: 29 AF XY: 0.0000139 AC XY: 10AN XY: 720572
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GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74490
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial temporal lobe epilepsy 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at