rs3767444

chr1-167723379-C-T

Variant summary

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

The NM_003953.6(MPZL1):c.91+1137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,112 control chromosomes in the GnomAD database, including 6,379 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 0.29 (6379 hom., cov: 33)
• Consequence: MPZL1 NM_003953.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

MPZL1 (HGNC:7226): (myelin protein zero like 1) Predicted to enable structural molecule activity. Predicted to be involved in cell-cell signaling and transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to act upstream of or within positive regulation of cell migration. Located in cell surface and focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPZL1	NM_003953.6	c.91+1137C>T		intron_variant		ENST00000359523.7
MPZL1	NM_001146191.2	c.91+1137C>T		intron_variant
MPZL1	NM_024569.5	c.91+1137C>T		intron_variant
MPZL1	XM_047433610.1	c.-364+1137C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPZL1	ENST00000359523.7	c.91+1137C>T		intron_variant		1	NM_003953.6	P3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43811 AN: 151994 Hom.: 6368 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.288 AC: 43873 AN: 152112 Hom.: 6379 Cov.: 33 AF XY: 0.285 AC XY: 21219 AN XY: 74360

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.310

Alfa AF: 0.289 Hom.: 3527

Bravo AF: 0.287

Asia WGS AF: 0.289 AC: 1004 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.4
Dann	Benign	0.27

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: rs3767444; hg19: chr1-167692616;