5-170775980-C-T

Variant names:

• chr5-170775980-C-T
• rs7722456
• ENST00000522868.5:c.-43+3326C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522868.5(GABRP):​c.-43+3326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,066 control chromosomes in the GnomAD database, including 45,790 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 0.77 (45790 hom., cov: 32)
• Consequence: GABRP ENST00000522868.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 9 publications found

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]

ENSG00000253348 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986475	XR_001742978.3	n.3610+3467G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRP	ENST00000522868.5	c.-43+3326C>T		intron_variant	Intron 1 of 6	5		ENSP00000430188.1
GABRP	ENST00000521481.5	c.-43+12466C>T		intron_variant	Intron 1 of 5	5		ENSP00000428804.1
GABRP	ENST00000521009.5	c.-43+11550C>T		intron_variant	Intron 1 of 4	4		ENSP00000428103.1

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117470 AN: 151948 Hom.: 45765 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.788

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.773 AC: 117538 AN: 152066 Hom.: 45790 Cov.: 32 AF XY: 0.776 AC XY: 57697 AN XY: 74336

African (AFR) AF: 0.698 AC: 28924 AN: 41456

American (AMR) AF: 0.818 AC: 12517 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2861 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5023 AN: 5182

South Asian (SAS) AF: 0.904 AC: 4349 AN: 4810

European-Finnish (FIN) AF: 0.752 AC: 7946 AN: 10566

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53286 AN: 67970

Other (OTH) AF: 0.779 AC: 1645 AN: 2112

Alfa AF: 0.782 Hom.: 94788

Bravo AF: 0.774

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7722456; hg19: chr5-170202984;