X-96884635-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_013347.4(RPA4):c.325G>C(p.Gly109Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000282 in 1,097,549 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 21)
  • Exomes 𝑓: 0.000028 (0 hom. 6 hem.)
• Consequence: RPA4 NM_013347.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0270

Genes affected

RPA4 (HGNC:30305): (replication protein A4) This gene encodes a single-stranded DNA-binding protein that is the 30-kDa subunit of the replication protein A complex. Replication protein A is an essential factor for DNA double-strand break repair and cell cycle checkpoint activation. The encoded protein localizes to DNA repair foci and may be involved in the cellular DNA damage response. This protein may also play a role in inhibiting viral replication.[provided by RefSeq, Apr 2010]

DIAPH2 (HGNC:2877): (diaphanous related formin 2) The product of this gene belongs to the diaphanous subfamily of the formin homology family of proteins. This gene may play a role in the development and normal function of the ovaries. Defects in this gene have been linked to premature ovarian failure 2. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0459857).
• BS2: High Hemizygotes in GnomAdExome at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPA4	NM_013347.4	c.325G>C	p.Gly109Arg	missense_variant	1/1	ENST00000373040.4
DIAPH2	NM_006729.5	c.587+2917G>C		intron_variant		ENST00000324765.13
DIAPH2	NM_007309.4	c.587+2917G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPA4	ENST00000373040.4	c.325G>C	p.Gly109Arg	missense_variant	1/1		NM_013347.4	P1
DIAPH2	ENST00000324765.13	c.587+2917G>C		intron_variant		1	NM_006729.5	A2
DIAPH2	ENST00000373049.8	c.587+2917G>C		intron_variant		1		P3

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD3 exomes AF: 0.000148 AC: 27 AN: 182819 Hom.: 0 AF XY: 0.0000890 AC XY: 6 AN XY: 67441

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000985

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000282 AC: 31 AN: 1097549 Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 6 AN XY: 362915

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000881

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 21

Alfa AF: 0.000142 Hom.: 1

Bravo AF: 0.0000756

ExAC AF: 0.000115 AC: 14

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 09, 2021

The c.325G>C (p.G109R) alteration is located in exon 1 (coding exon 1) of the RPA4 gene. This alteration results from a G to C substitution at nucleotide position 325, causing the glycine (G) at amino acid position 109 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-0.73
Cadd	Benign	9.9
Dann	Uncertain	0.99
DEOGEN2	Benign	0.0054	T
FATHMM_MKL	Benign	0.094	N
LIST_S2	Benign	0.32	T
M_CAP	Uncertain	0.13	D
MetaRNN	Benign	0.046	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.76	N
MutationTaster	Benign	1.0	N;N;N;N;N;N
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.41	N
REVEL	Benign	0.037
Sift	Uncertain	0.022	D
Sift4G	Uncertain	0.044	D
Polyphen		0.065	B
Vest4		0.12
MutPred		0.58		Gain of MoRF binding (P = 0.0179);
MVP		0.41
MPC		0.16
ClinPred		0.047	T
GERP RS		0.14
Varity_R		0.10
gMVP		0.049

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs761816138; hg19: chrX-96139634;