19-35299741-GC-AA

Position:

• chr19-35299741-GC-AA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_002361.4(MAG):​c.603_604delinsAA​(p.Leu202Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 25)
• Consequence: MAG NM_002361.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.52

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 19-35299741-GC-AA is Benign according to our data. Variant chr19-35299741-GC-AA is described in ClinVar as [Likely_benign]. Clinvar id is 475608.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAG	NM_002361.4	c.603_604delinsAA	p.Leu202Met	missense_variant	5/11	ENST00000392213.8	NP_002352.1
MAG	NM_001199216.2	c.528_529delinsAA	p.Leu177Met	missense_variant	5/11		NP_001186145.1
MAG	NM_080600.3	c.603_604delinsAA	p.Leu202Met	missense_variant	5/12		NP_542167.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAG	ENST00000392213.8	c.603_604delinsAA	p.Leu202Met	missense_variant	5/11	1	NM_002361.4	ENSP00000376048	P1
MAG	ENST00000361922.8	c.603_604delinsAA	p.Leu202Met	missense_variant	5/12	1		ENSP00000355234
MAG	ENST00000537831.2	c.528_529delinsAA	p.Leu177Met	missense_variant	5/11	1		ENSP00000440695
MAG	ENST00000597035.5	c.*187_*188delinsAA		3_prime_UTR_variant	5/5	4		ENSP00000473245

Frequencies

GnomAD3 genomes Cov.: 25

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 25

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary spastic paraplegia 75 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs36055167; hg19: chr19-35790644;