2-86984812-T-C

Position:

• chr2-86984812-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001382344.1(RGPD1):​c.2640T>C​(p.Tyr880=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.00032 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RGPD1 NM_001382344.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.90

Genes affected

RGPD1 (HGNC:32414): (RANBP2 like and GRIP domain containing 1) Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 2-86984812-T-C is Benign according to our data. Variant chr2-86984812-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2651105.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGPD1	NM_001382344.1	c.2640T>C	p.Tyr880=	synonymous_variant	19/23	ENST00000641458.2	NP_001369273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGPD1	ENST00000641458.2	c.2640T>C	p.Tyr880=	synonymous_variant	19/23		NM_001382344.1	ENSP00000492954	A2
RGPD1	ENST00000398193.8	c.2640T>C	p.Tyr880=	synonymous_variant	19/23	1		ENSP00000381253	P4
RGPD1	ENST00000428128.1	c.*559T>C		3_prime_UTR_variant, NMD_transcript_variant	6/10	1		ENSP00000402729

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.0000510 AC: 10 AN: 195986 Hom.: 0 AF XY: 0.0000832 AC XY: 9 AN XY: 108128

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.000119

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000215

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000419

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000325 AC: 266 AN: 819522 Hom.: 0 Cov.: 10 AF XY: 0.000477 AC XY: 201 AN XY: 421562

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000218

Gnomad4 ASJ exome AF: 0.00222

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00273

Gnomad4 FIN exome AF: 0.0000417

Gnomad4 NFE exome AF: 0.000101

Gnomad4 OTH exome AF: 0.000590

GnomAD4 genome Cov.: 0

Alfa AF: 0.000672 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

RGPD1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	8.5
DANN	Benign	0.57

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: rs763823852; hg19: chr2-87211935;