chr2-107871445-A-G

Variant names:

• chr2-107871445-A-G
• rs832358
• NM_182588.3:c.3441A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6_Very_Strong BP7

The NM_182588.3(RGPD4):​c.3441A>G​(p.Leu1147Leu) 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 Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.21 (1825 hom., cov: 4)
  • Exomes 𝑓: 0.48 (207130 hom.)
  • Failed GnomAD Quality Control
• Consequence: RGPD4 NM_182588.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

Genes affected

RGPD4 (HGNC:32417): (RANBP2 like and GRIP domain containing 4) 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]

LOC124906057 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 2-107871445-A-G is Benign according to our data. Variant chr2-107871445-A-G is described in ClinVar as Benign. ClinVar VariationId is 403374.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.078 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182588.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGPD4	NM_182588.3	MANE Select	c.3441A>G	p.Leu1147Leu	synonymous	Exon 20 of 23	NP_872394.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGPD4	ENST00000408999.4	TSL:1 MANE Select	c.3441A>G	p.Leu1147Leu	synonymous	Exon 20 of 23	ENSP00000386810.4	Q7Z3J3-1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 6689 AN: 32558 Hom.: 1812 Cov.: 4

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.250

GnomAD2 exomes AF: 0.215 AC: 28750 AN: 133662 AF XY: 0.205

Gnomad AFR exome AF: 0.683

Gnomad AMR exome AF: 0.159

Gnomad ASJ exome AF: 0.228

Gnomad EAS exome AF: 0.0632

Gnomad FIN exome AF: 0.0503

Gnomad NFE exome AF: 0.225

Gnomad OTH exome AF: 0.293

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.480 AC: 426449 AN: 888328 Hom.: 207130 Cov.: 30 AF XY: 0.492 AC XY: 217879 AN XY: 442976

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.817 AC: 14574 AN: 17830

American (AMR) AF: 0.298 AC: 8928 AN: 29928

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 10891 AN: 16134

East Asian (EAS) AF: 0.225 AC: 6180 AN: 27476

South Asian (SAS) AF: 0.692 AC: 35130 AN: 50768

European-Finnish (FIN) AF: 0.572 AC: 15846 AN: 27726

Middle Eastern (MID) AF: 0.680 AC: 1733 AN: 2548

European-Non Finnish (NFE) AF: 0.460 AC: 311946 AN: 678024

Other (OTH) AF: 0.560 AC: 21221 AN: 37894

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.206 AC: 6702 AN: 32568 Hom.: 1825 Cov.: 4 AF XY: 0.186 AC XY: 3013 AN XY: 16212

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.419 AC: 1828 AN: 4362

American (AMR) AF: 0.166 AC: 828 AN: 4976

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 134 AN: 588

East Asian (EAS) AF: 0.106 AC: 341 AN: 3202

South Asian (SAS) AF: 0.340 AC: 311 AN: 916

European-Finnish (FIN) AF: 0.105 AC: 291 AN: 2776

Middle Eastern (MID) AF: 0.541 AC: 40 AN: 74

European-Non Finnish (NFE) AF: 0.184 AC: 2772 AN: 15046

Other (OTH) AF: 0.248 AC: 125 AN: 504

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.383 Hom.: 909

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.9
DANN	Benign	0.58
PhyloP100		0.078
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs832358; hg19: chr2-108487901; COSMIC: COSV61744327;