rs369690599

Variant names:

• chr6-127475550-C-G
• rs369690599
• ENST00000525778.6:c.2476G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-127475550-C-G
• chr6-127475550-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001400265.1(MTCL3):​c.2476G>C​(p.Gly826Arg) 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. G826S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MTCL3 NM_001400265.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.89

Genes affected

SOGA3 (HGNC:21494): (MTCL family member 3) Predicted to be involved in regulation of autophagy. Predicted to be located in extracellular space. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255330 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.30676425).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTCL3	NM_001400265.1	c.2476G>C	p.Gly826Arg	missense_variant	Exon 6 of 7		NP_001387194.1
SOGA3-KIAA0408	NR_174482.1	n.3321G>C		non_coding_transcript_exon_variant	Exon 6 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOGA3	ENST00000525778.6	c.2476G>C	p.Gly826Arg	missense_variant	Exon 6 of 7	5		ENSP00000434570.1
ENSG00000255330	ENST00000481848.6	n.2476G>C		non_coding_transcript_exon_variant	Exon 6 of 12	5		ENSP00000455908.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Benign	-0.044	T
BayesDel_noAF	Benign	-0.30
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Benign	0.043	T;T
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.56
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Benign	0.021	T
MetaRNN	Benign	0.31	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.8	L;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-2.3	N;N
REVEL	Benign	0.16
Sift	Uncertain	0.0080	D;D
Sift4G	Uncertain	0.036	D;D
Polyphen		0.98	D;.
Vest4		0.51
MutPred		0.22		Gain of MoRF binding (P = 0.0166);Gain of MoRF binding (P = 0.0166);
MVP		0.19
ClinPred		0.91	D
GERP RS		5.3
Varity_R		0.24
gMVP		0.99

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: rs369690599; hg19: chr6-127796695;