1-183698997-A-G

Position:

• chr1-183698997-A-G

Variant summary

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

The ENST00000304685.8(RGL1):​c.-32-43129A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,196 control chromosomes in the GnomAD database, including 32,855 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 0.65 (32855 hom., cov: 34)
• Consequence: RGL1 ENST00000304685.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGL1	NM_001297669.3	c.-33+1485A>G		intron_variant
RGL1	NM_001297670.3	c.-32-43129A>G		intron_variant
RGL1	NM_015149.6	c.-32-43129A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGL1	ENST00000304685.8	c.-32-43129A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99573 AN: 152078 Hom.: 32821 Cov.: 34

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.655 AC: 99654 AN: 152196 Hom.: 32855 Cov.: 34 AF XY: 0.657 AC XY: 48934 AN XY: 74426

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.658

Alfa AF: 0.615 Hom.: 36897

Bravo AF: 0.660

Asia WGS AF: 0.734 AC: 2550 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.63

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: rs6424904; hg19: chr1-183668132;