chr9-127189862-G-A

Variant names:

• chr9-127189862-G-A
• rs1890546
• NM_014636.3:c.911-5229G>A

Variant summary

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

The NM_014636.3(RALGPS1):​c.911-5229G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,154 control chromosomes in the GnomAD database, including 21,639 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 0.53 (21639 hom., cov: 33)
• Consequence: RALGPS1 NM_014636.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 7 publications found

Genes affected

RALGPS1 (HGNC:16851): (Ral GEF with PH domain and SH3 binding motif 1) Enables guanyl-nucleotide exchange factor activity. Involved in regulation of Ral protein signal transduction. Predicted to be located in cytoplasm and plasma 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014636.3. 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
	RALGPS1	NM_014636.3	MANE Select	c.911-5229G>A		intron	N/A	NP_055451.1	Q5JS13-1
	RALGPS1	NM_001322325.2		c.911-5229G>A		intron	N/A	NP_001309254.1
	RALGPS1	NM_001322321.2		c.911-5229G>A		intron	N/A	NP_001309250.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALGPS1	ENST00000259351.10	TSL:1 MANE Select	c.911-5229G>A		intron	N/A	ENSP00000259351.5	Q5JS13-1
	RALGPS1	ENST00000373434.5	TSL:1	c.911-5229G>A		intron	N/A	ENSP00000362533.1	Q5JS13-2
	RALGPS1	ENST00000903176.1		c.911-5229G>A		intron	N/A	ENSP00000573235.1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80213 AN: 152036 Hom.: 21618 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.528 AC: 80292 AN: 152154 Hom.: 21639 Cov.: 33 AF XY: 0.527 AC XY: 39242 AN XY: 74398

African (AFR) AF: 0.510 AC: 21144 AN: 41474

American (AMR) AF: 0.575 AC: 8796 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3470

East Asian (EAS) AF: 0.710 AC: 3684 AN: 5186

South Asian (SAS) AF: 0.716 AC: 3453 AN: 4824

European-Finnish (FIN) AF: 0.388 AC: 4114 AN: 10598

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35328 AN: 67990

Other (OTH) AF: 0.581 AC: 1229 AN: 2116

Alfa AF: 0.531 Hom.: 11102

Bravo AF: 0.541

Asia WGS AF: 0.688 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.32
PhyloP100		-0.22
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: rs1890546; hg19: chr9-129952141;