rs7744005

Positions:

• chr6-89404422-G-T

Variant summary

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

The NM_021244.5(RRAGD):​c.148+7424C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,016 control chromosomes in the GnomAD database, including 6,769 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 0.28 (6769 hom., cov: 31)
• Consequence: RRAGD NM_021244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RRAGD	NM_021244.5	c.148+7424C>A		intron_variant		ENST00000369415.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RRAGD	ENST00000369415.9	c.148+7424C>A		intron_variant		1	NM_021244.5	P1
RRAGD	ENST00000359203.3	c.-10+7424C>A		intron_variant		2
RRAGD	ENST00000492783.1	n.172+6912C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42324 AN: 151898 Hom.: 6753 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.279 AC: 42373 AN: 152016 Hom.: 6769 Cov.: 31 AF XY: 0.276 AC XY: 20494 AN XY: 74322

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0741

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.269

Alfa AF: 0.241 Hom.: 2494

Bravo AF: 0.282

Asia WGS AF: 0.207 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.81

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: rs7744005; hg19: chr6-90114141; COSMIC: COSV63270222;