Variant rs1128933 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006715.4(MAN2C1):c.2370C>T(p.Asp790Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 1,613,224 control chromosomes in the GnomAD database, including 178,303 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 0.37 ( 12553 hom., cov: 33)

Exomes 𝑓: 0.47 ( 165750 hom. )

Consequence

MAN2C1
NM_006715.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0410

Variant links:

Genes affected

MAN2C1 (HGNC:6827): (mannosidase alpha class 2C member 1) Predicted to enable alpha-mannosidase activity. Predicted to be involved in oligosaccharide catabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MAN2C1 links:

MAN2C1 (HGNC:):

MAN2C1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-0.041 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAN2C1	NM_006715.4 linkuse as main transcript	c.2370C>T	p.Asp790Asp	synonymous_variant	20/26	ENST00000267978.10	NP_006706.2	Q9NTJ4-1A0A140VJN9
MAN2C1	NM_001256494.2 linkuse as main transcript	c.2421C>T	p.Asp807Asp	synonymous_variant	20/26		NP_001243423.1	Q9NTJ4-4
MAN2C1	NM_001256495.2 linkuse as main transcript	c.2370C>T	p.Asp790Asp	synonymous_variant	20/26		NP_001243424.1	Q9NTJ4-2
MAN2C1	NM_001256496.2 linkuse as main transcript	c.2073C>T	p.Asp691Asp	synonymous_variant	18/24		NP_001243425.1	Q9NTJ4-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAN2C1	ENST00000267978.10 linkuse as main transcript	c.2370C>T	p.Asp790Asp	synonymous_variant	20/26	1	NM_006715.4	ENSP00000267978.4		Q9NTJ4-1

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56206

AN:

151994

Hom.:

12560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.536

Gnomad FIN

AF:

0.476

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.370

GnomAD3 exomes

AF:

0.467

AC:

117155

AN:

250700

Hom.:

28775

AF XY:

0.478

AC XY:

64829

AN XY:

135642

show subpopulations

Gnomad AFR exome

AF:

0.0975

Gnomad AMR exome

AF:

0.499

Gnomad ASJ exome

AF:

0.420

Gnomad EAS exome

AF:

0.503

Gnomad SAS exome

AF:

0.543

Gnomad FIN exome

AF:

0.487

Gnomad NFE exome

AF:

0.484

Gnomad OTH exome

AF:

0.470

GnomAD4 exome

AF:

0.471

AC:

688048

AN:

1461112

Hom.:

165750

Cov.:

AF XY:

0.474

AC XY:

344849

AN XY:

726866

show subpopulations

Gnomad4 AFR exome

AF:

0.0843

Gnomad4 AMR exome

AF:

0.488

Gnomad4 ASJ exome

AF:

0.423

Gnomad4 EAS exome

AF:

0.444

Gnomad4 SAS exome

AF:

0.542

Gnomad4 FIN exome

AF:

0.487

Gnomad4 NFE exome

AF:

0.479

Gnomad4 OTH exome

AF:

0.446

GnomAD4 genome

AF:

0.369

AC:

56187

AN:

152112

Hom.:

12553

Cov.:

AF XY:

0.372

AC XY:

27668

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.419

Gnomad4 ASJ

AF:

0.422

Gnomad4 EAS

AF:

0.482

Gnomad4 SAS

AF:

0.535

Gnomad4 FIN

AF:

0.476

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.365

Alfa

AF:

0.454

Hom.:

21079

Bravo

AF:

0.354

Asia WGS

AF:

0.477

AC:

1662

AN:

3478

EpiCase

AF:

0.473

EpiControl

AF:

0.479

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.40

DANN

Benign

0.85

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over