11-68690475-C-T

Position:

• chr11-68690475-C-T

Variant summary

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

The NM_015973.5(GAL):​c.302-442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,938 control chromosomes in the GnomAD database, including 30,051 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 0.61 (30051 hom., cov: 31)
• Consequence: GAL NM_015973.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAL	NM_015973.5	c.302-442C>T		intron_variant		ENST00000265643.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAL	ENST00000265643.4	c.302-442C>T		intron_variant		1	NM_015973.5	P1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93380 AN: 151820 Hom.: 30044 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.607

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.615 AC: 93415 AN: 151938 Hom.: 30051 Cov.: 31 AF XY: 0.627 AC XY: 46620 AN XY: 74304

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.609

Alfa AF: 0.622 Hom.: 4285

Bravo AF: 0.588

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.11
DANN	Benign	0.70

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: rs3136541; hg19: chr11-68457943;