rs1062108

Positions:

• chr6-89365640-A-G

Variant summary

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

The NM_021244.5(RRAGD):​c.*2416T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,106 control chromosomes in the GnomAD database, including 36,480 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 0.68 (36480 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: RRAGD NM_021244.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

RRAGD (HGNC:19903): (Ras related GTP binding D) RRAGD is a monomeric guanine nucleotide-binding protein, or G protein. By binding GTP or GDP, small G proteins act as molecular switches in numerous cell processes and signaling pathways.[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RRAGD	NM_021244.5	c.*2416T>C		3_prime_UTR_variant	7/7	ENST00000369415.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RRAGD	ENST00000369415.9	c.*2416T>C		3_prime_UTR_variant	7/7	1	NM_021244.5	P1
RRAGD	ENST00000359203.3	c.*2416T>C		3_prime_UTR_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103288 AN: 151988 Hom.: 36416 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.628

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.680 AC: 103408 AN: 152106 Hom.: 36480 Cov.: 32 AF XY: 0.677 AC XY: 50324 AN XY: 74354

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.633

Alfa AF: 0.607 Hom.: 58157

Bravo AF: 0.682

Asia WGS AF: 0.689 AC: 2396 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.53

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: rs1062108; hg19: chr6-90075359;