chr9-5660807-C-T

Position:

• chr9-5660807-C-T

Variant summary

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

The NM_020829.4(RIC1):​c.252+4117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,796 control chromosomes in the GnomAD database, including 17,393 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 0.47 (17393 hom., cov: 31)
• Consequence: RIC1 NM_020829.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

Genes affected

RIC1 (HGNC:17686): (RIC1 homolog, RAB6A GEF complex partner 1) Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in several processes, including positive regulation of GTPase activity; regulation of extracellular matrix constituent secretion; and retrograde transport, endosome to Golgi. Located in cytosol and membrane. Part of Ric1-Rgp1 guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Apr 2022]

RIC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIC1	NM_020829.4	c.252+4117C>T		intron_variant		ENST00000414202.7	NP_065880.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIC1	ENST00000414202.7	c.252+4117C>T		intron_variant		5	NM_020829.4	ENSP00000416696.2
RIC1	ENST00000545641.5	c.36+4117C>T		intron_variant		1		ENSP00000439488.1
RIC1	ENST00000251879.10	c.252+4117C>T		intron_variant		1		ENSP00000251879.6
RIC1	ENST00000418622.7	c.252+4117C>T		intron_variant		5		ENSP00000402240.4

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71552 AN: 151676 Hom.: 17355 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.472 AC: 71647 AN: 151796 Hom.: 17393 Cov.: 31 AF XY: 0.473 AC XY: 35113 AN XY: 74182

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.444

Alfa AF: 0.412 Hom.: 5503

Bravo AF: 0.482

Asia WGS AF: 0.517 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.55

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: rs7026868; hg19: chr9-5660807;