rs11084424

chr19-56180202-C-Achr19-56180202-C-T

Variant summary

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

The NM_033106.4(GALP):c.88-384C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,166 control chromosomes in the GnomAD database, including 4,239 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 0.22 (4239 hom., cov: 33)
• Consequence: GALP NM_033106.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

Genes affected

GALP (HGNC:24840): (galanin like peptide) This gene encodes a member of the galanin family of neuropeptides. The encoded protein binds galanin receptors 1, 2 and 3 with the highest affinity for galanin receptor 3 and has been implicated in biological processes involving the central nervous system including hypothalamic regulation of metabolism and reproduction. A peptide encoded by a splice variant of this gene, termed alarin, has vasoactive properties, displays antimicrobial activity against E. coli, and may serve as a marker for neuroblastic tumors.[provided by RefSeq, Nov 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALP	NM_033106.4	c.88-384C>A		intron_variant		ENST00000357330.7
GALP	NM_001145546.2	c.88-1970C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALP	ENST00000357330.7	c.88-384C>A		intron_variant		1	NM_033106.4	P2
GALP	ENST00000590002.1	c.88-1970C>A		intron_variant		1		A2
GALP	ENST00000440823.1	c.88-1970C>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32886 AN: 152046 Hom.: 4225 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.216 AC: 32923 AN: 152166 Hom.: 4239 Cov.: 33 AF XY: 0.222 AC XY: 16505 AN XY: 74386

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.222

Alfa AF: 0.205 Hom.: 3097

Bravo AF: 0.220

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.99
Dann	Benign	0.52

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: rs11084424; hg19: chr19-56691571;