ENST00000304685.8:c.-32-39440C>T

Variant names:

• chr1-183702686-C-T
• rs12092963
• ENST00000304685.8:c.-32-39440C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000304685.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGL1	NM_015149.6		c.-32-39440C>T		intron	N/A	NP_055964.3
	RGL1	NM_001297669.3		c.-33+5174C>T		intron	N/A	NP_001284598.1
	RGL1	NM_001297670.3		c.-32-39440C>T		intron	N/A	NP_001284599.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGL1	ENST00000304685.8	TSL:1	c.-32-39440C>T		intron	N/A	ENSP00000303192.3

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

African (AFR) AF: 0.351 AC: 14523 AN: 41418

American (AMR) AF: 0.198 AC: 3022 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3472

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5182

South Asian (SAS) AF: 0.133 AC: 642 AN: 4822

European-Finnish (FIN) AF: 0.124 AC: 1310 AN: 10582

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0967 AC: 6575 AN: 67980

Other (OTH) AF: 0.180 AC: 380 AN: 2108

Alfa AF: 0.159 Hom.: 349

Bravo AF: 0.194

Asia WGS AF: 0.117 AC: 408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.0
DANN	Benign	0.49
PhyloP100		1.6
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: rs12092963; hg19: chr1-183671821;