rs771957751

Variant names:

• chr8-41537223-G-A
• rs771957751
• NM_032336.3:c.227G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-41537223-G-A
• chr8-41537223-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032336.3(GINS4):​c.227G>A​(p.Ser76Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: GINS4 NM_032336.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.50

Genes affected

GINS4 (HGNC:28226): (GINS complex subunit 4) The yeast heterotetrameric GINS complex is made up of Sld5, Psf1 (GINS1; MIM 610608), Psf2 (GINS2; MIM 610609), and Psf3 (GINS3; MIM 610610). The formation of the GINS complex is essential for the initiation of DNA replication in yeast and Xenopus egg extracts (Ueno et al., 2005 [PubMed 16287864]). See GINS1 for additional information about the GINS complex.[supplied by OMIM, Mar 2008]

GPAT4-AS1 (HGNC:55539): (GPAT4 and GINS4 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20246369).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GINS4	NM_032336.3	c.227G>A	p.Ser76Asn	missense_variant	Exon 4 of 8	ENST00000276533.4	NP_115712.1
GINS4	XM_005273659.5	c.227G>A	p.Ser76Asn	missense_variant	Exon 4 of 8		XP_005273716.1
GPAT4-AS1	NR_125824.1	n.151C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GINS4	ENST00000276533.4	c.227G>A	p.Ser76Asn	missense_variant	Exon 4 of 8	1	NM_032336.3	ENSP00000276533.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.080	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.11	T;.;T;.
Eigen	Benign	-0.12
Eigen_PC	Benign	0.012
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.78	T;T;.;T
M_CAP	Benign	0.0061	T
MetaRNN	Benign	0.20	T;T;T;T
MetaSVM	Benign	-0.89	T
MutationAssessor	Uncertain	2.1	M;M;M;.
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-1.1	N;N;N;N
REVEL	Benign	0.11
Sift	Benign	0.30	T;T;T;T
Sift4G	Benign	0.57	T;T;T;T
Polyphen		0.0010	B;.;B;.
Vest4		0.48
MutPred		0.61		Loss of phosphorylation at S76 (P = 0.0404);Loss of phosphorylation at S76 (P = 0.0404);Loss of phosphorylation at S76 (P = 0.0404);Loss of phosphorylation at S76 (P = 0.0404);
MVP		0.46
MPC		0.24
ClinPred		0.91	D
GERP RS		3.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.23
gMVP		0.51

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: rs771957751; hg19: chr8-41394742;