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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001480.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALR1	NM_001480.4	MANE Select	c.*4320G>T		3_prime_UTR	Exon 3 of 3	NP_001471.2	P47211

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALR1	ENST00000299727.5	TSL:1 MANE Select	c.*4320G>T		3_prime_UTR	Exon 3 of 3	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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over