rs12092963

chr1-183702686-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000304685.8(RGL1):c.-32-39440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,052 control chromosomes in the GnomAD database, including 3,370 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 0.18 (3370 hom., cov: 32)
• Consequence: RGL1 ENST00000304685.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

RGL1 (HGNC:30281): (ral guanine nucleotide dissociation stimulator like 1) Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGL1	NM_001297669.3	c.-33+5174C>T		intron_variant
RGL1	NM_001297670.3	c.-32-39440C>T		intron_variant
RGL1	NM_015149.6	c.-32-39440C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGL1	ENST00000304685.8	c.-32-39440C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27213 AN: 151934 Hom.: 3349 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.179 AC: 27283 AN: 152052 Hom.: 3370 Cov.: 32 AF XY: 0.178 AC XY: 13269 AN XY: 74362

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0967

Gnomad4 OTH AF: 0.180

Alfa AF: 0.152 Hom.: 312

Bravo AF: 0.194

Asia WGS AF: 0.117 AC: 408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	4.0
Dann	Benign	0.49

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

Other links and lift over

dbSNP: rs12092963; hg19: chr1-183671821;