rs2584820

Variant names:

• chr1-182469951-A-G
• rs2584820
• NM_001137669.2:c.302-2445A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

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 = 0.248 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001137669.2. 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
	RGSL1	NM_001137669.2	MANE Select	c.302-2445A>G		intron	N/A	NP_001131141.1	A5PLK6-1
	RGSL1	NM_001366934.1		c.302-1331A>G		intron	N/A	NP_001353863.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGSL1	ENST00000294854.13	TSL:1 MANE Select	c.302-2445A>G		intron	N/A	ENSP00000457748.1	A5PLK6-1
	RGSL1	ENST00000634679.1	TSL:5	c.-56-2445A>G		intron	N/A	ENSP00000489502.1	A0A0U1RRF6
	RGSL1	ENST00000634758.1	TSL:5	c.-68-3624A>G		intron	N/A	ENSP00000488942.1	A0A0U1RQD8

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

African (AFR) AF: 0.0876 AC: 3639 AN: 41530

American (AMR) AF: 0.118 AC: 1808 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1336 AN: 5156

South Asian (SAS) AF: 0.0657 AC: 317 AN: 4826

European-Finnish (FIN) AF: 0.0580 AC: 614 AN: 10588

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3847 AN: 67990

Other (OTH) AF: 0.0789 AC: 167 AN: 2116

Alfa AF: 0.0653 Hom.: 50

Bravo AF: 0.0892

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		-0.61
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: rs2584820; hg19: chr1-182439086;