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rs1497575

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173536.4(GABRG1):c.253+5867C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,854 control chromosomes in the GnomAD database, including 30,135 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 0.61 ( 30135 hom., cov: 31)

Consequence

GABRG1
NM_173536.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412
Variant links:
Genes affected
GABRG1 (HGNC:4086): (gamma-aminobutyric acid type A receptor subunit gamma1) The protein encoded by this gene belongs to the ligand-gated ionic channel family. It is an integral membrane protein and plays an important role in inhibiting neurotransmission by binding to the benzodiazepine receptor and opening an integral chloride channel. This gene is clustered with three other family members on chromosome 4. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GABRG1NM_173536.4 linkuse as main transcriptc.253+5867C>T intron_variant ENST00000295452.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GABRG1ENST00000295452.5 linkuse as main transcriptc.253+5867C>T intron_variant 1 NM_173536.4 P1

Frequencies

GnomAD3 genomes
AF:
0.611
AC:
92660
AN:
151736
Hom.:
30085
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.835
Gnomad AMI
AF:
0.470
Gnomad AMR
AF:
0.549
Gnomad ASJ
AF:
0.424
Gnomad EAS
AF:
0.367
Gnomad SAS
AF:
0.349
Gnomad FIN
AF:
0.598
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.541
Gnomad OTH
AF:
0.562
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.611
AC:
92771
AN:
151854
Hom.:
30135
Cov.:
31
AF XY:
0.606
AC XY:
44948
AN XY:
74162
show subpopulations
Gnomad4 AFR
AF:
0.835
Gnomad4 AMR
AF:
0.549
Gnomad4 ASJ
AF:
0.424
Gnomad4 EAS
AF:
0.367
Gnomad4 SAS
AF:
0.349
Gnomad4 FIN
AF:
0.598
Gnomad4 NFE
AF:
0.541
Gnomad4 OTH
AF:
0.558
Alfa
AF:
0.535
Hom.:
29367
Bravo
AF:
0.618
Asia WGS
AF:
0.397
AC:
1382
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.64
Dann
Benign
0.67

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.

Other links and lift over

dbSNP: rs1497575; hg19: chr4-46093351; API