chr19-33026246-G-A

Variant names:

• chr19-33026246-G-A
• rs28570619
• NM_033103.5:c.314+258C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033103.5(RHPN2):​c.314+258C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 151,756 control chromosomes in the GnomAD database, including 718 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 0.087 (718 hom., cov: 30)
• Consequence: RHPN2 NM_033103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 3 publications found

Genes affected

RHPN2 (HGNC:19974): (rhophilin Rho GTPase binding protein 2) This gene encodes a member of the rhophilin family of Ras-homologous (Rho)-GTPase binding proteins. The encoded protein binds both GTP- and GDP-bound RhoA and GTP-bound RhoB and may be involved in the organization of the actin cytoskeleton. [provided by RefSeq, Apr 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RHPN2	NM_033103.5	c.314+258C>T		intron_variant	Intron 3 of 14	ENST00000254260.8	NP_149094.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RHPN2	ENST00000254260.8	c.314+258C>T		intron_variant	Intron 3 of 14	1	NM_033103.5	ENSP00000254260.2
RHPN2	ENST00000544458.6	n.768+258C>T		intron_variant	Intron 1 of 11	2
RHPN2	ENST00000588388.5	n.314+258C>T		intron_variant	Intron 3 of 13	2		ENSP00000465898.1

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13257 AN: 151636 Hom.: 718 Cov.: 30

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0874 AC: 13268 AN: 151756 Hom.: 718 Cov.: 30 AF XY: 0.0916 AC XY: 6790 AN XY: 74164

African (AFR) AF: 0.116 AC: 4796 AN: 41368

American (AMR) AF: 0.0965 AC: 1469 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.143 AC: 737 AN: 5146

South Asian (SAS) AF: 0.230 AC: 1106 AN: 4800

European-Finnish (FIN) AF: 0.0683 AC: 719 AN: 10522

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0543 AC: 3687 AN: 67928

Other (OTH) AF: 0.0879 AC: 185 AN: 2104

Alfa AF: 0.0513 Hom.: 61

Bravo AF: 0.0892

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-0.18
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: rs28570619; hg19: chr19-33517152;