rs10502228

chr11-118242868-C-T

Variant summary

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

The NM_198275.3(MPZL3):c.74-2491G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,090 control chromosomes in the GnomAD database, including 3,421 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 0.21 (3421 hom., cov: 32)
• Consequence: MPZL3 NM_198275.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

Genes affected

MPZL3 (HGNC:27279): (myelin protein zero like 3) Predicted to be involved in cell adhesion. Predicted to act upstream of or within extracellular matrix organization and hair cycle. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPZL3	NM_198275.3	c.74-2491G>A		intron_variant		ENST00000278949.9
MPZL3	NM_001286152.2	c.74-2527G>A		intron_variant
MPZL3	NR_104404.2	n.145-9345G>A		intron_variant, non_coding_transcript_variant
MPZL3	NR_104405.2	n.145-2491G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPZL3	ENST00000278949.9	c.74-2491G>A		intron_variant		1	NM_198275.3	P1
MPZL3	ENST00000525386.5	c.74-9345G>A		intron_variant		1
MPZL3	ENST00000527472.1	c.74-2527G>A		intron_variant		1
MPZL3	ENST00000446386.2	c.74-2491G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31829 AN: 151972 Hom.: 3409 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.210 AC: 31895 AN: 152090 Hom.: 3421 Cov.: 32 AF XY: 0.209 AC XY: 15538 AN XY: 74340

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0886

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.219

Alfa AF: 0.206 Hom.: 5431

Bravo AF: 0.219

Asia WGS AF: 0.136 AC: 472 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	8.1
Dann	Benign	0.59

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: rs10502228; hg19: chr11-118113583;