Variant chr18-77250689-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001480.4(GALR1):c.141T>C(p.Gly47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 1,612,500 control chromosomes in the GnomAD database, including 308,168 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 0.57 ( 25560 hom., cov: 33)

Exomes 𝑓: 0.62 ( 282608 hom. )

Consequence

GALR1
NM_001480.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.280

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:

LOC124904329 (HGNC:):

LOC124904329 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=-0.28 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
GALR1	NM_001480.4 linkuse as main transcript	c.141T>C	p.Gly47=	synonymous_variant	1/3	ENST00000299727.5	NP_001471.2
LOC124904329	XR_007066422.1 linkuse as main transcript	n.604+159A>G		intron_variant, non_coding_transcript_variant
GALR1	XM_017025691.2 linkuse as main transcript	c.141T>C	p.Gly47=	synonymous_variant	1/3		XP_016881180.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALR1	ENST00000299727.5 linkuse as main transcript	c.141T>C	p.Gly47=	synonymous_variant	1/3	1	NM_001480.4	ENSP00000299727	P1

Frequencies

GnomAD3 genomes

AF:

0.570

AC:

86675

AN:

151944

Hom.:

25555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.520

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.773

Gnomad EAS

AF:

0.350

Gnomad SAS

AF:

0.527

Gnomad FIN

AF:

0.631

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.648

Gnomad OTH

AF:

0.586

GnomAD3 exomes

AF:

0.570

AC:

141504

AN:

248438

Hom.:

42022

AF XY:

0.582

AC XY:

78365

AN XY:

134720

show subpopulations

Gnomad AFR exome

AF:

0.481

Gnomad AMR exome

AF:

0.375

Gnomad ASJ exome

AF:

0.761

Gnomad EAS exome

AF:

0.370

Gnomad SAS exome

AF:

0.561

Gnomad FIN exome

AF:

0.618

Gnomad NFE exome

AF:

0.649

Gnomad OTH exome

AF:

0.593

GnomAD4 exome

AF:

0.617

AC:

900605

AN:

1460438

Hom.:

282608

Cov.:

AF XY:

0.618

AC XY:

448799

AN XY:

726572

show subpopulations

Gnomad4 AFR exome

AF:

0.480

Gnomad4 AMR exome

AF:

0.385

Gnomad4 ASJ exome

AF:

0.758

Gnomad4 EAS exome

AF:

0.320

Gnomad4 SAS exome

AF:

0.562

Gnomad4 FIN exome

AF:

0.624

Gnomad4 NFE exome

AF:

0.641

Gnomad4 OTH exome

AF:

0.619

GnomAD4 genome

AF:

0.570

AC:

86713

AN:

152062

Hom.:

25560

Cov.:

AF XY:

0.569

AC XY:

42324

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.481

Gnomad4 ASJ

AF:

0.773

Gnomad4 EAS

AF:

0.350

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.631

Gnomad4 NFE

AF:

0.648

Gnomad4 OTH

AF:

0.580

Alfa

AF:

0.634

Hom.:

64572

Bravo

AF:

0.553

Asia WGS

AF:

0.423

AC:

1470

AN:

3476

EpiCase

AF:

0.658

EpiControl

AF:

0.662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.70

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over