rs200984385

Variant names:

• chr19-35299784-G-A
• NM_002361.4:c.646G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-35299784-G-A
• chr19-35299784-G-T

Variant summary

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

The NM_002361.4(MAG):​c.646G>A​(p.Gly216Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000718 in 1,393,514 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 25)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: MAG NM_002361.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.14

Genes affected

MAG (HGNC:6783): (myelin associated glycoprotein) The protein encoded by this gene is a type I membrane protein and member of the immunoglobulin superfamily. It is thought to be involved in the process of myelination. It is a lectin that binds to sialylated glycoconjugates and mediates certain myelin-neuron cell-cell interactions. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAG	NM_002361.4	c.646G>A	p.Gly216Ser	missense_variant	Exon 5 of 11	ENST00000392213.8	NP_002352.1
MAG	NM_001199216.2	c.571G>A	p.Gly191Ser	missense_variant	Exon 5 of 11		NP_001186145.1
MAG	NM_080600.3	c.646G>A	p.Gly216Ser	missense_variant	Exon 5 of 12		NP_542167.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAG	ENST00000392213.8	c.646G>A	p.Gly216Ser	missense_variant	Exon 5 of 11	1	NM_002361.4	ENSP00000376048.2

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome AF: 7.18e-7 AC: 1 AN: 1393514 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 687938

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000276

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Benign	0.0072	T
BayesDel_noAF	Benign	-0.23
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	T;.;.
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.35
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.80	T;T;T
M_CAP	Pathogenic	0.31	D
MetaRNN	Uncertain	0.52	D;D;D
MetaSVM	Benign	-0.66	T
MutationAssessor	Benign	1.2	L;L;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	1.0	N;N;N
REVEL	Uncertain	0.36
Sift	Benign	0.17	T;T;T
Sift4G	Benign	0.26	T;T;T
Polyphen		0.96	D;.;.
Vest4		0.34
MutPred		0.69		Gain of disorder (P = 0.1188);Gain of disorder (P = 0.1188);.;
MVP		0.50
MPC		0.98
ClinPred		0.89	D
GERP RS		4.6
Varity_R		0.31
gMVP		0.70

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-35790687;