Variant rs1042577 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015973.5(GAL):c.*15T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 1,557,318 control chromosomes in the GnomAD database, including 340,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.62 ( 30650 hom., cov: 32)

Exomes 𝑓: 0.66 ( 309826 hom. )

Consequence

GAL
NM_015973.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.47

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:

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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=-0.83).

BP6

Variant 11-68691002-T-C is Benign according to our data. Variant chr11-68691002-T-C is described in ClinVar as [Benign]. Clinvar id is 1285292.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAL	NM_015973.5 linkuse as main transcript	c.*15T>C		3_prime_UTR_variant	6/6	ENST00000265643.4	NP_057057.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAL	ENST00000265643.4 linkuse as main transcript	c.*15T>C		3_prime_UTR_variant	6/6	1	NM_015973.5	ENSP00000265643	P1

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

94323

AN:

151974

Hom.:

30645

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.668

Gnomad AMR

AF:

0.666

Gnomad ASJ

AF:

0.677

Gnomad EAS

AF:

0.780

Gnomad SAS

AF:

0.654

Gnomad FIN

AF:

0.884

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.613

GnomAD3 exomes

AF:

0.683

AC:

171367

AN:

250952

Hom.:

59884

AF XY:

0.682

AC XY:

92502

AN XY:

135720

show subpopulations

Gnomad AFR exome

AF:

0.429

Gnomad AMR exome

AF:

0.715

Gnomad ASJ exome

AF:

0.672

Gnomad EAS exome

AF:

0.781

Gnomad SAS exome

AF:

0.643

Gnomad FIN exome

AF:

0.876

Gnomad NFE exome

AF:

0.669

Gnomad OTH exome

AF:

0.674

GnomAD4 exome

AF:

0.661

AC:

928517

AN:

1405226

Hom.:

309826

Cov.:

AF XY:

0.660

AC XY:

463532

AN XY:

702288

show subpopulations

Gnomad4 AFR exome

AF:

0.428

Gnomad4 AMR exome

AF:

0.711

Gnomad4 ASJ exome

AF:

0.675

Gnomad4 EAS exome

AF:

0.768

Gnomad4 SAS exome

AF:

0.637

Gnomad4 FIN exome

AF:

0.870

Gnomad4 NFE exome

AF:

0.654

Gnomad4 OTH exome

AF:

0.648

GnomAD4 genome

AF:

0.620

AC:

94357

AN:

152092

Hom.:

30650

Cov.:

AF XY:

0.633

AC XY:

47062

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.435

Gnomad4 AMR

AF:

0.667

Gnomad4 ASJ

AF:

0.677

Gnomad4 EAS

AF:

0.780

Gnomad4 SAS

AF:

0.652

Gnomad4 FIN

AF:

0.884

Gnomad4 NFE

AF:

0.665

Gnomad4 OTH

AF:

0.615

Alfa

AF:

0.654

Hom.:

67994

Bravo

AF:

0.593

Asia WGS

AF:

0.710

AC:

2469

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Familial temporal lobe epilepsy 8

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.16

DANN

Benign

0.35

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

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