1-183927827-T-C

Variant names:

• chr1-183927827-T-C
• rs4650
• NM_001297671.3:c.*1535T>C

Variant summary

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

The NM_001297671.3(RGL1):​c.*1535T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,376 control chromosomes in the GnomAD database, including 25,993 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 0.58 (25921 hom., cov: 32)
  • Exomes 𝑓: 0.58 (72 hom.)
• Consequence: RGL1 NM_001297671.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001297671.3. 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_001297671.3	MANE Select	c.*1535T>C		3_prime_UTR	Exon 18 of 18	NP_001284600.1	Q9NZL6-1
	RGL1	NM_015149.6		c.*1535T>C		3_prime_UTR	Exon 19 of 19	NP_055964.3
	RGL1	NM_001297669.3		c.*1535T>C		3_prime_UTR	Exon 19 of 19	NP_001284598.1	B7Z2W5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGL1	ENST00000360851.4	TSL:1 MANE Select	c.*1535T>C		3_prime_UTR	Exon 18 of 18	ENSP00000354097.3	Q9NZL6-1
	RGL1	ENST00000304685.8	TSL:1	c.*1535T>C		3_prime_UTR	Exon 19 of 19	ENSP00000303192.3	Q9NZL6-2
	RGL1	ENST00000888235.1		c.*1535T>C		3_prime_UTR	Exon 19 of 19	ENSP00000558294.1

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88545 AN: 151826 Hom.: 25892 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.581 AC: 251 AN: 432 Hom.: 72 Cov.: 0 AF XY: 0.604 AC XY: 157 AN XY: 260

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.577 AC: 246 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.583 AC: 88624 AN: 151944 Hom.: 25921 Cov.: 32 AF XY: 0.583 AC XY: 43267 AN XY: 74250

African (AFR) AF: 0.621 AC: 25711 AN: 41428

American (AMR) AF: 0.536 AC: 8194 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1767 AN: 3466

East Asian (EAS) AF: 0.567 AC: 2927 AN: 5164

South Asian (SAS) AF: 0.568 AC: 2737 AN: 4816

European-Finnish (FIN) AF: 0.621 AC: 6543 AN: 10540

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38783 AN: 67936

Other (OTH) AF: 0.574 AC: 1213 AN: 2114

Alfa AF: 0.565 Hom.: 31152

Bravo AF: 0.576

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.45
PhyloP100		-1.4
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: rs4650; hg19: chr1-183896961;