rs7258661

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000357330.7(GALP):​c.88-354C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,166 control chromosomes in the GnomAD database, including 2,073 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 0.16 ( 2073 hom., cov: 32)

Consequence

GALP
ENST00000357330.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.416
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GALPNM_033106.4 linkuse as main transcriptc.88-354C>A intron_variant ENST00000357330.7 NP_149097.1
GALPNM_001145546.2 linkuse as main transcriptc.88-1940C>A intron_variant NP_001139018.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GALPENST00000357330.7 linkuse as main transcriptc.88-354C>A intron_variant 1 NM_033106.4 ENSP00000349884 P2Q9UBC7-1
GALPENST00000590002.1 linkuse as main transcriptc.88-1940C>A intron_variant 1 ENSP00000464698 A2Q9UBC7-2
GALPENST00000440823.1 linkuse as main transcriptc.88-1940C>A intron_variant 5 ENSP00000411521 A2Q9UBC7-2

Frequencies

GnomAD3 genomes
AF:
0.156
AC:
23735
AN:
152048
Hom.:
2076
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.226
Gnomad AMI
AF:
0.0857
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.117
Gnomad EAS
AF:
0.0202
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.126
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.142
Gnomad OTH
AF:
0.156
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.156
AC:
23735
AN:
152166
Hom.:
2073
Cov.:
32
AF XY:
0.155
AC XY:
11517
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.226
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.0201
Gnomad4 SAS
AF:
0.120
Gnomad4 FIN
AF:
0.126
Gnomad4 NFE
AF:
0.142
Gnomad4 OTH
AF:
0.157
Alfa
AF:
0.138
Hom.:
1922
Bravo
AF:
0.159
Asia WGS
AF:
0.0810
AC:
283
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.7
DANN
Benign
0.49

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7258661; hg19: chr19-56691601; API