Genetic Variant GALR1:c.*4320G>T (chr18-77273222-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001480.4(GALR1):c.*4320G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,344 control chromosomes in the GnomAD database, including 62,222 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 0.90 ( 62117 hom., cov: 30)

Exomes 𝑓: 0.96 ( 105 hom. )

Consequence

GALR1
NM_001480.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81

Publications

2 publications found

Variant links:

Genes affected

GALR1 (HGNC:4132): (galanin receptor 1) The neuropeptide galanin elicits a range of biological effects by interaction with specific G-protein-coupled receptors. Galanin receptors are seven-transmembrane proteins shown to activate a variety of intracellular second-messenger pathways. GALR1 inhibits adenylyl cyclase via a G protein of the Gi/Go family. GALR1 is widely expressed in the brain and spinal cord, as well as in peripheral sites such as the small intestine and heart. [provided by RefSeq, Jul 2008]

GALR1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALR1	NM_001480.4 link	c.*4320G>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000299727.5	NP_001471.2	P47211

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALR1	ENST00000299727.5 link	c.*4320G>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_001480.4	ENSP00000299727.3		P47211

Frequencies

GnomAD3 genomes

AF:

0.899

AC:

136716

AN:

152002

Hom.:

62070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.783

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.894

Gnomad ASJ

AF:

0.930

Gnomad EAS

AF:

0.825

Gnomad SAS

AF:

0.760

Gnomad FIN

AF:

0.985

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.971

Gnomad OTH

AF:

0.901

GnomAD4 exome

AF:

0.964

AC:

216

AN:

224

Hom.:

105

Cov.:

AF XY:

0.980

AC XY:

147

AN XY:

150

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.985

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.970

AC:

130

AN:

134

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.899

AC:

136825

AN:

152120

Hom.:

62117

Cov.:

AF XY:

0.899

AC XY:

66891

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.783

AC:

32453

AN:

41448

American (AMR)

AF:

0.894

AC:

13679

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.930

AC:

3228

AN:

3472

East Asian (EAS)

AF:

0.825

AC:

4252

AN:

5152

South Asian (SAS)

AF:

0.759

AC:

3648

AN:

4804

European-Finnish (FIN)

AF:

0.985

AC:

10447

AN:

10608

Middle Eastern (MID)

AF:

0.861

AC:

253

AN:

294

European-Non Finnish (NFE)

AF:

0.971

AC:

66049

AN:

68024

Other (OTH)

AF:

0.902

AC:

1905

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

641

1282

1924

2565

3206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.946

Hom.:

112228

Bravo

AF:

0.887

Asia WGS

AF:

0.793

AC:

2760

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.076

(source)

DANN

Benign

0.53

PhyloP100

-1.8

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over