rs200160606

Variant names:

• chr1-204198471-C-G
• rs200160606
• NM_198447.2:c.386G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-204198471-C-G
• chr1-204198471-C-T

Variant summary

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

The NM_198447.2(GOLT1A):​c.386G>C​(p.Ser129Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. S129N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GOLT1A NM_198447.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29
• Publications: 2 publications found

Genes affected

GOLT1A (HGNC:24766): (golgi transport 1A) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Located in Golgi apparatus subcompartment; endoplasmic reticulum; and nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

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=0.12648559).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198447.2. 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
	GOLT1A	NM_198447.2	MANE Select	c.386G>C	p.Ser129Thr	missense	Exon 5 of 5	NP_940849.1	Q6ZVE7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLT1A	ENST00000308302.4	TSL:1 MANE Select	c.386G>C	p.Ser129Thr	missense	Exon 5 of 5	ENSP00000308535.3	Q6ZVE7
	GOLT1A	ENST00000874691.1		c.518G>C	p.Ser173Thr	missense	Exon 5 of 5	ENSP00000544750.1
	GOLT1A	ENST00000936492.1		c.143G>C	p.Ser48Thr	missense	Exon 3 of 3	ENSP00000606551.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	19
DANN	Benign	0.94
DEOGEN2	Benign	0.24	T
Eigen	Benign	-0.073
Eigen_PC	Benign	0.074
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.53	T
M_CAP	Benign	0.0036	T
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-0.91	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		2.3
PrimateAI	Benign	0.44	T
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.098
Sift	Benign	0.30	T
Sift4G	Benign	0.098	T
Polyphen		0.0010	B
Vest4		0.15
MutPred		0.15		Gain of glycosylation at S129 (P = 0.0279)
MVP		0.030
MPC		0.30
ClinPred		0.83	D
GERP RS		5.0
Varity_R		0.17
gMVP		0.55
Mutation Taster		=67/33	polymorphism

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: rs200160606; hg19: chr1-204167599;