rs7249617

chr19-35305081-C-Gchr19-35305081-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002361.4(MAG):c.1231+2373C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,196 control chromosomes in the GnomAD database, including 431 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.044 (431 hom., cov: 32)
• Consequence: MAG NM_002361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAG	NM_002361.4	c.1231+2373C>G		intron_variant		ENST00000392213.8
MAG	NM_001199216.2	c.1156+2373C>G		intron_variant
MAG	NM_080600.3	c.1231+2373C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAG	ENST00000392213.8	c.1231+2373C>G		intron_variant		1	NM_002361.4	P1
MAG	ENST00000361922.8	c.1231+2373C>G		intron_variant		1
MAG	ENST00000537831.2	c.1156+2373C>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6654 AN: 152078 Hom.: 433 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0141

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000750

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0438 AC: 6666 AN: 152196 Hom.: 431 Cov.: 32 AF XY: 0.0425 AC XY: 3164 AN XY: 74408

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.0649

Gnomad4 SAS AF: 0.0334

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.000750

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.000777 Hom.: 1

Bravo AF: 0.0488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.1
Dann	Benign	0.37

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: rs7249617; hg19: chr19-35795984;