10-43208426-G-C

Variant names:

• chr10-43208426-G-C
• rs10793422
• NM_145313.4:c.-6-2304C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_145313.4(RASGEF1A):​c.-6-2304C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: RASGEF1A NM_145313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

Genes affected

RASGEF1A (HGNC:24246): (RasGEF domain family member 1A) Enables guanyl-nucleotide exchange factor activity. Involved in cell migration and positive regulation of Ras protein signal transduction. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASGEF1A	NM_145313.4	c.-6-2304C>G		intron_variant	Intron 1 of 12	ENST00000395810.6	NP_660356.2
RASGEF1A	NM_001282862.2	c.19-2304C>G		intron_variant	Intron 1 of 12		NP_001269791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASGEF1A	ENST00000395810.6	c.-6-2304C>G		intron_variant	Intron 1 of 12	1	NM_145313.4	ENSP00000379155.1
RASGEF1A	ENST00000395809.5	c.-1749C>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 13	2		ENSP00000379154.1
RASGEF1A	ENST00000395809.5	c.-1749C>G		5_prime_UTR_variant	Exon 1 of 13	2		ENSP00000379154.1
RASGEF1A	ENST00000374459.5	c.19-2304C>G		intron_variant	Intron 1 of 12	2		ENSP00000363583.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.72

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: rs10793422; hg19: chr10-43703874;