Variant chr5-170789133-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_014211.3(GABRP):c.58T>C(p.Cys20Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,458,850 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

GABRP
NM_014211.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.38

Variant links:

Genes affected

GABRP (HGNC:4089): (gamma-aminobutyric acid type A receptor subunit pi) The gamma-aminobutyric acid (GABA) A receptor is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. The subunit encoded by this gene is expressed in several non-neuronal tissues including the uterus and ovaries. This subunit can assemble with known GABA A receptor subunits, and the presence of this subunit alters the sensitivity of recombinant receptors to modulatory agents such as pregnanolone. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

GABRP links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
GABRP	NM_014211.3 linkuse as main transcript	c.58T>C	p.Cys20Arg	missense_variant	3/10	ENST00000265294.9
GABRP	NM_001291985.2 linkuse as main transcript	c.58T>C	p.Cys20Arg	missense_variant	3/9
GABRP	XM_024446012.2 linkuse as main transcript	c.58T>C	p.Cys20Arg	missense_variant	3/10
GABRP	XM_005265872.2 linkuse as main transcript	c.-66+465T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRP	ENST00000265294.9 linkuse as main transcript	c.58T>C	p.Cys20Arg	missense_variant	3/10	1	NM_014211.3	P1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251160

Hom.:

AF XY:

0.00

AC XY:

AN XY:

135746

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000880

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000411

AC:

AN:

1458850

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

725888

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000270

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

Cov.:

Alfa

AF:

0.000111

Hom.:

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 13, 2024

The c.58T>C (p.C20R) alteration is located in exon 3 (coding exon 2) of the GABRP gene. This alteration results from a T to C substitution at nucleotide position 58, causing the cysteine (C) at amino acid position 20 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Uncertain

0.075

BayesDel_noAF

Benign

-0.13

CADD

Benign

DANN

Benign

0.76

DEOGEN2

Benign

0.17

.;.;.;.;T;.;T;.;.

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.61

FATHMM_MKL

Benign

0.67

LIST_S2

Benign

0.58

T;T;T;T;.;T;T;T;T

M_CAP

Benign

0.032

MetaRNN

Uncertain

0.72

D;D;D;D;D;D;D;D;D

MetaSVM

Benign

-0.80

MutationAssessor

Benign

0.55

.;.;.;.;N;.;N;.;.

MutationTaster

Benign

0.99

D;D;D;D

PrimateAI

Uncertain

0.63

PROVEAN

Benign

-0.57

N;N;D;N;N;D;N;N;N

REVEL

Uncertain

0.36

Sift

Uncertain

0.0040

D;D;D;D;D;D;D;D;T

Sift4G

Benign

0.073

T;T;D;T;D;D;D;T;T

Polyphen

0.0

.;.;.;.;B;.;B;B;.

Vest4

0.37, 0.39, 0.34, 0.33

MutPred

0.84

Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);Gain of disorder (P = 0.0397);

MVP

0.62

MPC

0.21

ClinPred

0.11

GERP RS

1.4

Varity_R

0.48

gMVP

0.54

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