rs1034597

Positions:

• chr19-35308297-T-C

Variant summary

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

The NM_002361.4(MAG):​c.1232-1577T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,090 control chromosomes in the GnomAD database, including 43,605 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 0.75 (43605 hom., cov: 33)
• Consequence: MAG NM_002361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAG	NM_002361.4	c.1232-1577T>C		intron_variant		ENST00000392213.8
MAG	NM_001199216.2	c.1157-1577T>C		intron_variant
MAG	NM_080600.3	c.1232-1577T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAG	ENST00000392213.8	c.1232-1577T>C		intron_variant		1	NM_002361.4	P1
MAG	ENST00000361922.8	c.1232-1577T>C		intron_variant		1
MAG	ENST00000537831.2	c.1157-1577T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113558 AN: 151972 Hom.: 43551 Cov.: 33

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.747 AC: 113672 AN: 152090 Hom.: 43605 Cov.: 33 AF XY: 0.742 AC XY: 55169 AN XY: 74326

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.771

Alfa AF: 0.702 Hom.: 40663

Bravo AF: 0.757

Asia WGS AF: 0.701 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.29

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: rs1034597; hg19: chr19-35799200;