rs7177101

chr15-38507168-G-A

Variant summary

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

The NM_005739.4(RASGRP1):c.1242+558C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,986 control chromosomes in the GnomAD database, including 15,441 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 0.44 (15441 hom., cov: 32)
• Consequence: RASGRP1 NM_005739.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489

Genes affected

RASGRP1 (HGNC:9878): (RAS guanyl releasing protein 1) This gene is a member of a family of genes characterized by the presence of a Ras superfamily guanine nucleotide exchange factor (GEF) domain. It functions as a diacylglycerol (DAG)-regulated nucleotide exchange factor specifically activating Ras through the exchange of bound GDP for GTP. It activates the Erk/MAP kinase cascade and regulates T-cells and B-cells development, homeostasis and differentiation. Alternatively spliced transcript variants encoding different isoforms have been identified. Altered expression of the different isoforms of this protein may be a cause of susceptibility to systemic lupus erythematosus (SLE). [provided by RefSeq, Jul 2008]

LOC105370774 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASGRP1	NM_005739.4	c.1242+558C>T		intron_variant		ENST00000310803.10
LOC105370774	XR_001751485.3	n.2941+852G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASGRP1	ENST00000310803.10	c.1242+558C>T		intron_variant		1	NM_005739.4	P1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66689 AN: 151868 Hom.: 15397 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.439 AC: 66789 AN: 151986 Hom.: 15441 Cov.: 32 AF XY: 0.445 AC XY: 33053 AN XY: 74280

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.407

Alfa AF: 0.369 Hom.: 22280

Bravo AF: 0.442

Asia WGS AF: 0.631 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.5
Dann	Benign	0.35

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: rs7177101; hg19: chr15-38799369;