10-97865671-G-T

Variant names:

• chr10-97865671-G-T
• rs759330644
• NM_001010917.3:c.475G>T

Variant summary

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

The NM_001010917.3(GOLGA7B):​c.475G>T​(p.Gly159Cys) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G159S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GOLGA7B NM_001010917.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.86
• Publications: 0 publications found

Genes affected

GOLGA7B (HGNC:31668): (golgin A7 family member B) Enables enzyme binding activity. Predicted to be involved in peptidyl-L-cysteine S-palmitoylation and protein targeting to membrane. Predicted to be located in Golgi membrane. Predicted to be part of palmitoyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

CRTAC1 (HGNC:14882): (cartilage acidic protein 1) This gene encodes a glycosylated extracellular matrix protein that is found in the interterritorial matrix of articular deep zone cartilage. This protein is used as a marker to distinguish chondrocytes from osteoblasts and mesenchymal stem cells in culture. The presence of FG-GAP motifs and an RGD integrin-binding motif suggests that this protein may be involved in cell-cell or cell-matrix interactions. Copy number alterations in this gene have been observed in neurofibromatosis type 1-associated glomus tumors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

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=0.1724141).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010917.3. 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
	GOLGA7B	NM_001010917.3	MANE Select	c.475G>T	p.Gly159Cys	missense	Exon 5 of 5	NP_001010917.1	Q2TAP0
	CRTAC1	NM_018058.7	MANE Select	c.1863C>A	p.Thr621Thr	synonymous	Exon 15 of 15	NP_060528.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA7B	ENST00000370602.6	TSL:1 MANE Select	c.475G>T	p.Gly159Cys	missense	Exon 5 of 5	ENSP00000359634.1	Q2TAP0
	CRTAC1	ENST00000370597.8	TSL:1 MANE Select	c.1863C>A	p.Thr621Thr	synonymous	Exon 15 of 15	ENSP00000359629.3	Q9NQ79-1
	CRTAC1	ENST00000413387.5	TSL:2	c.1508C>A	p.Pro503Gln	missense	Exon 12 of 12	ENSP00000408445.1	Q5T4F6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.060
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0012	T
Eigen	Benign	0.013
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.58	T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PhyloP100		3.9
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	0.030	N
REVEL	Benign	0.12
Sift	Benign	0.079	T
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.31
MutPred		0.24		Loss of relative solvent accessibility (P = 0.0186)
MVP		0.23
MPC		0.42
ClinPred		0.89	D
GERP RS		4.5
Varity_R		0.20
gMVP		0.76
Mutation Taster		=83/17	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs759330644; hg19: chr10-99625428;