1-183867898-A-G

Variant names:

• chr1-183867898-A-G
• rs4651156
• NM_001297671.3:c.425+1825A>G

Variant summary

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

The NM_001297671.3(RGL1):​c.425+1825A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,118 control chromosomes in the GnomAD database, including 32,937 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 0.64 (32937 hom., cov: 32)
• Consequence: RGL1 NM_001297671.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 9 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGL1	NM_001297671.3	c.425+1825A>G		intron_variant	Intron 4 of 17	ENST00000360851.4	NP_001284600.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGL1	ENST00000360851.4	c.425+1825A>G		intron_variant	Intron 4 of 17	1	NM_001297671.3	ENSP00000354097.3
RGL1	ENST00000304685.8	c.530+1825A>G		intron_variant	Intron 5 of 18	1		ENSP00000303192.3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97085 AN: 152000 Hom.: 32948 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.638 AC: 97100 AN: 152118 Hom.: 32937 Cov.: 32 AF XY: 0.646 AC XY: 48003 AN XY: 74360

African (AFR) AF: 0.386 AC: 16004 AN: 41462

American (AMR) AF: 0.713 AC: 10896 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2220 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4542 AN: 5174

South Asian (SAS) AF: 0.756 AC: 3645 AN: 4820

European-Finnish (FIN) AF: 0.778 AC: 8232 AN: 10576

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49384 AN: 68012

Other (OTH) AF: 0.649 AC: 1369 AN: 2110

Alfa AF: 0.697 Hom.: 177711

Bravo AF: 0.623

Asia WGS AF: 0.783 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4651156; hg19: chr1-183837032;