rs694066

Positions:

• chr11-68685517-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015973.5(GAL):​c.82-77G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 985,366 control chromosomes in the GnomAD database, including 6,241 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 0.14 (2478 hom., cov: 33)
  • Exomes 𝑓: 0.083 (3763 hom.)
• Consequence: GAL NM_015973.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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]

LOC107984343 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAL	NM_015973.5	c.82-77G>A		intron_variant		ENST00000265643.4
LOC107984343	XR_001748281.1	n.230+2324C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAL	ENST00000265643.4	c.82-77G>A		intron_variant		1	NM_015973.5	P1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21521 AN: 152140 Hom.: 2473 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.0531

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.0832 AC: 69275 AN: 833108 Hom.: 3763 AF XY: 0.0819 AC XY: 35857 AN XY: 437990

Gnomad4 AFR exome AF: 0.321

Gnomad4 AMR exome AF: 0.0603

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.0157

Gnomad4 SAS exome AF: 0.0649

Gnomad4 FIN exome AF: 0.0313

Gnomad4 NFE exome AF: 0.0848

Gnomad4 OTH exome AF: 0.0989

GnomAD4 genome AF: 0.141 AC: 21544 AN: 152258 Hom.: 2478 Cov.: 33 AF XY: 0.136 AC XY: 10105 AN XY: 74446

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0528

Gnomad4 FIN AF: 0.0228

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.125

Alfa AF: 0.128 Hom.: 322

Bravo AF: 0.154

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.76

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

Other links and lift over

dbSNP: rs694066; hg19: chr11-68452985;