1-183698997-A-G

Variant names:

• chr1-183698997-A-G
• rs6424904
• ENST00000304685.8:c.-32-43129A>G

Variant summary

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

The NM_015149.6(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 NM_015149.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 8 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015149.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGL1	NM_015149.6		c.-32-43129A>G		intron	N/A	NP_055964.3
	RGL1	NM_001297669.3		c.-33+1485A>G		intron	N/A	NP_001284598.1	B7Z2W5
	RGL1	NM_001297670.3		c.-32-43129A>G		intron	N/A	NP_001284599.1	B7Z2W5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGL1	ENST00000304685.8	TSL:1	c.-32-43129A>G		intron	N/A	ENSP00000303192.3	Q9NZL6-2

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

African (AFR) AF: 0.708 AC: 29414 AN: 41524

American (AMR) AF: 0.684 AC: 10457 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2235 AN: 3472

East Asian (EAS) AF: 0.790 AC: 4091 AN: 5180

South Asian (SAS) AF: 0.663 AC: 3195 AN: 4820

European-Finnish (FIN) AF: 0.637 AC: 6749 AN: 10590

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41278 AN: 67994

Other (OTH) AF: 0.658 AC: 1392 AN: 2114

Alfa AF: 0.620 Hom.: 48084

Bravo AF: 0.660

Asia WGS AF: 0.734 AC: 2550 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.63
PhyloP100		-0.78
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6424904;

hg19: chr1-183668132;