rs2584820

Positions:

• chr1-182469951-A-G

Variant summary

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

The NM_001137669.2(RGSL1):​c.302-2445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,150 control chromosomes in the GnomAD database, including 641 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 0.079 (641 hom., cov: 32)
• Consequence: RGSL1 NM_001137669.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

Genes affected

RGSL1 (HGNC:18636): (regulator of G protein signaling like 1) Predicted to be integral component of membrane. [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 = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGSL1	NM_001137669.2	c.302-2445A>G		intron_variant		ENST00000294854.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGSL1	ENST00000294854.13	c.302-2445A>G		intron_variant		1	NM_001137669.2	P1

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 11931 AN: 152032 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0786 AC: 11953 AN: 152150 Hom.: 641 Cov.: 32 AF XY: 0.0797 AC XY: 5931 AN XY: 74402

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0580

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.0789

Alfa AF: 0.0645 Hom.: 48

Bravo AF: 0.0892

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.44

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: rs2584820; hg19: chr1-182439086;