2-107868322-A-G

Variant names:

• chr2-107868322-A-G
• rs3876806
• NM_182588.3:c.2606-1561A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000408999.4(RGPD4):​c.2606-1561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00012 (0 hom., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: RGPD4 ENST00000408999.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000408999.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGPD4	NM_182588.3	MANE Select	c.2606-1561A>G		intron	N/A	NP_872394.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGPD4	ENST00000408999.4	TSL:1 MANE Select	c.2606-1561A>G		intron	N/A	ENSP00000386810.4

Frequencies

GnomAD3 genomes AF: 0.000107 AC: 13 AN: 121944 Hom.: 0 Cov.: 17

Gnomad AFR AF: 0.0000933

Gnomad AMI AF: 0.00122

Gnomad AMR AF: 0.0000901

Gnomad ASJ AF: 0.000329

Gnomad EAS AF: 0.00101

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000513

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000123 AC: 15 AN: 122016 Hom.: 0 Cov.: 17 AF XY: 0.000121 AC XY: 7 AN XY: 58058

African (AFR) AF: 0.000155 AC: 5 AN: 32252

American (AMR) AF: 0.0000899 AC: 1 AN: 11122

Ashkenazi Jewish (ASJ) AF: 0.000329 AC: 1 AN: 3036

East Asian (EAS) AF: 0.00102 AC: 4 AN: 3940

South Asian (SAS) AF: 0.00 AC: 0 AN: 3244

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7392

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 238

European-Non Finnish (NFE) AF: 0.0000513 AC: 3 AN: 58434

Other (OTH) AF: 0.00 AC: 0 AN: 1540

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.32
PhyloP100		0.032

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: rs3876806; hg19: chr2-108484778;