Genetic Variant GAL:c.301+16T>C (chr11-68688942-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015973.5(GAL):c.301+16T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 1,207,036 control chromosomes in the GnomAD database, including 330,269 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 40005 hom., cov: 32)

Exomes 𝑓: 0.74 ( 290264 hom. )

Consequence

GAL
NM_015973.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.245

Variant links:

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]

GAL links:

LOC107984343 (HGNC:):

LOC107984343 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 11-68688942-T-C is Benign according to our data. Variant chr11-68688942-T-C is described in ClinVar as [Benign]. Clinvar id is 1285291.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAL	NM_015973.5 link	c.301+16T>C		intron_variant	Intron 5 of 5	ENST00000265643.4	NP_057057.2
LOC107984343	XR_001748281.1 link	n.-84A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAL	ENST00000265643.4 link	c.301+16T>C		intron_variant	Intron 5 of 5	1	NM_015973.5	ENSP00000265643.3		P22466

Frequencies

GnomAD3 genomes

AF:

0.720

AC:

109473

AN:

151992

Hom.:

39974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.610

Gnomad AMI

AF:

0.774

Gnomad AMR

AF:

0.739

Gnomad ASJ

AF:

0.759

Gnomad EAS

AF:

0.855

Gnomad SAS

AF:

0.787

Gnomad FIN

AF:

0.905

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.737

Gnomad OTH

AF:

0.716

GnomAD3 exomes

AF:

0.764

AC:

189041

AN:

247436

Hom.:

72817

AF XY:

0.765

AC XY:

102294

AN XY:

133752

show subpopulations

Gnomad AFR exome

AF:

0.604

Gnomad AMR exome

AF:

0.783

Gnomad ASJ exome

AF:

0.757

Gnomad EAS exome

AF:

0.845

Gnomad SAS exome

AF:

0.776

Gnomad FIN exome

AF:

0.897

Gnomad NFE exome

AF:

0.740

Gnomad OTH exome

AF:

0.754

GnomAD4 exome

AF:

0.739

AC:

779785

AN:

1054926

Hom.:

290264

Cov.:

AF XY:

0.741

AC XY:

402106

AN XY:

542526

show subpopulations

Gnomad4 AFR exome

AF:

0.595

Gnomad4 AMR exome

AF:

0.780

Gnomad4 ASJ exome

AF:

0.756

Gnomad4 EAS exome

AF:

0.846

Gnomad4 SAS exome

AF:

0.770

Gnomad4 FIN exome

AF:

0.893

Gnomad4 NFE exome

AF:

0.722

Gnomad4 OTH exome

AF:

0.738

GnomAD4 genome

AF:

0.720

AC:

109553

AN:

152110

Hom.:

40005

Cov.:

AF XY:

0.730

AC XY:

54286

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.611

Gnomad4 AMR

AF:

0.739

Gnomad4 ASJ

AF:

0.759

Gnomad4 EAS

AF:

0.854

Gnomad4 SAS

AF:

0.786

Gnomad4 FIN

AF:

0.905

Gnomad4 NFE

AF:

0.737

Gnomad4 OTH

AF:

0.717

Alfa

AF:

0.716

Hom.:

8927

Bravo

AF:

0.700

Asia WGS

AF:

0.811

AC:

2820

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Familial temporal lobe epilepsy 8

Benign:2

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.4

DANN

Benign

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over