chr19-56180202-C-A

Variant names:

• chr19-56180202-C-A
• rs11084424
• NM_033106.4:c.88-384C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033106.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALP	NM_033106.4	MANE Select	c.88-384C>A		intron	N/A	NP_149097.1
	GALP	NM_001145546.2		c.88-1970C>A		intron	N/A	NP_001139018.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALP	ENST00000357330.7	TSL:1 MANE Select	c.88-384C>A		intron	N/A	ENSP00000349884.2
	GALP	ENST00000590002.1	TSL:1	c.88-1970C>A		intron	N/A	ENSP00000464698.1
	GALP	ENST00000440823.1	TSL:5	c.88-1970C>A		intron	N/A	ENSP00000411521.1

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

African (AFR) AF: 0.127 AC: 5295 AN: 41552

American (AMR) AF: 0.308 AC: 4707 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3468

East Asian (EAS) AF: 0.604 AC: 3112 AN: 5150

South Asian (SAS) AF: 0.244 AC: 1180 AN: 4828

European-Finnish (FIN) AF: 0.248 AC: 2624 AN: 10578

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14558 AN: 67996

Other (OTH) AF: 0.222 AC: 469 AN: 2112

Alfa AF: 0.212 Hom.: 5240

Bravo AF: 0.220

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.99
DANN	Benign	0.52
PhyloP100		-0.91
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11084424; hg19: chr19-56691571;