9-128276155-C-G

Variant names:

• chr9-128276155-C-G
• rs371883568
• NM_001379267.1:c.90-432C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001379267.1(SWI5):​c.90-432C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000706 in 1,416,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: SWI5 NM_001379267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 0 publications found

Genes affected

SWI5 (HGNC:31412): (SWI5 homologous recombination repair protein) Involved in cellular response to ionizing radiation and double-strand break repair via homologous recombination. Part of Swi5-Sfr1 complex. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA2 (HGNC:4425): (golgin A2) The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. This gene encodes one of the golgins, a family of proteins localized to the Golgi. This encoded protein has been postulated to play roles in the stacking of Golgi cisternae and in vesicular transport. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of these variants has not been determined. [provided by RefSeq, Feb 2010]

GOLGA2 Gene-Disease associations (from GenCC):

• developmental delay with hypotonia, myopathy, and brain abnormalities

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08606687).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001379267.1. 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
	SWI5	NM_001379267.1		c.90-432C>G		intron	N/A	NP_001366196.1
	SWI5	NM_001318092.2		c.90-552C>G		intron	N/A	NP_001305021.1	H7C5E9
	GOLGA2	NM_001366244.2	MANE Select	c.-179G>C		upstream_gene	N/A	NP_001353173.2	A0A8J9BZL8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SWI5	ENST00000372898.6	TSL:5	c.57-552C>G		intron	N/A	ENSP00000361989.2	H3BLW9
	SWI5	ENST00000495313.5	TSL:3	c.90-552C>G		intron	N/A	ENSP00000419719.2	H7C5E9
	GOLGA2	ENST00000611957.5	TSL:1 MANE Select	c.-179G>C		upstream_gene	N/A	ENSP00000478799.2	A0A8J9BZL8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.06e-7 AC: 1 AN: 1416106 Hom.: 0 Cov.: 33 AF XY: 0.00000143 AC XY: 1 AN XY: 700568

African (AFR) AF: 0.00 AC: 0 AN: 31390

American (AMR) AF: 0.00 AC: 0 AN: 35290

Ashkenazi Jewish (ASJ) AF: 0.0000424 AC: 1 AN: 23612

East Asian (EAS) AF: 0.00 AC: 0 AN: 39076

South Asian (SAS) AF: 0.00 AC: 0 AN: 81332

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52014

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5530

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1089642

Other (OTH) AF: 0.00 AC: 0 AN: 58220

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Uncertain	0.013	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	0.50
DANN	Benign	0.92
DEOGEN2	Benign	0.0040	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.33	N
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.031	D
MetaRNN	Benign	0.086	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.55	N
PhyloP100		-1.7
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.60	N
REVEL	Benign	0.046
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		0.56	P
Vest4		0.17
MutPred		0.20		Loss of solvent accessibility (P = 0.0329)
MVP		0.14
MPC		0.30
ClinPred		0.22	T
GERP RS		0.74
PromoterAI		-0.032	Neutral
Varity_R		0.082
gMVP		0.014

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: rs371883568; hg19: chr9-131038434;