rs10079475

Variant names:

• chr5-180158240-A-G
• rs10079475
• NM_175062.4:c.-6-20182T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-180158240-A-G
• chr5-180158240-A-T

Variant summary

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

The NM_175062.4(RASGEF1C):​c.-6-20182T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,130 control chromosomes in the GnomAD database, including 1,850 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 0.15 (1850 hom., cov: 32)
• Consequence: RASGEF1C NM_175062.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

RASGEF1C (HGNC:27400): (RasGEF domain family member 1C) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity and small GTPase mediated signal transduction. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASGEF1C	NM_175062.4	c.-6-20182T>C		intron_variant	Intron 1 of 13	ENST00000361132.9	NP_778232.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASGEF1C	ENST00000361132.9	c.-6-20182T>C		intron_variant	Intron 1 of 13	1	NM_175062.4	ENSP00000354963.4
RASGEF1C	ENST00000615330.4	c.-459-20182T>C		intron_variant	Intron 1 of 14	5		ENSP00000481349.1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22858 AN: 152010 Hom.: 1849 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.150 AC: 22872 AN: 152130 Hom.: 1850 Cov.: 32 AF XY: 0.151 AC XY: 11221 AN XY: 74352

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.121

Alfa AF: 0.142 Hom.: 368

Bravo AF: 0.143

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.38

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: rs10079475; hg19: chr5-179585240;