Variant chr3-187221168-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001879.6(MASP1):c.1810-34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,521,678 control chromosomes in the GnomAD database, including 70,287 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10926 hom., cov: 32)

Exomes 𝑓: 0.28 ( 59361 hom. )

Consequence

MASP1
NM_001879.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.424

Variant links:

Genes affected

MASP1 (HGNC:6901): (MBL associated serine protease 1) This gene encodes a serine protease that functions as a component of the lectin pathway of complement activation. The complement pathway plays an essential role in the innate and adaptive immune response. The encoded protein is synthesized as a zymogen and is activated when it complexes with the pathogen recognition molecules of lectin pathway, the mannose-binding lectin and the ficolins. This protein is not directly involved in complement activation but may play a role as an amplifier of complement activation by cleaving complement C2 or by activating another complement serine protease, MASP-2. The encoded protein is also able to cleave fibrinogen and factor XIII and may may be involved in coagulation. A splice variant of this gene which lacks the serine protease domain functions as an inhibitor of the complement pathway. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]

MASP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 3-187221168-C-T is Benign according to our data. Variant chr3-187221168-C-T is described in ClinVar as [Benign]. Clinvar id is 1222412.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MASP1	NM_001879.6 linkuse as main transcript	c.1810-34G>A		intron_variant		ENST00000337774.10	NP_001870.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MASP1	ENST00000337774.10 linkuse as main transcript	c.1810-34G>A		intron_variant		1	NM_001879.6	ENSP00000336792	P1	P48740-1

Frequencies

GnomAD3 genomes

AF:

0.355

AC:

53934

AN:

152012

Hom.:

10900

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.271

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.689

Gnomad SAS

AF:

0.365

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.375

GnomAD3 exomes

AF:

0.341

AC:

76259

AN:

223682

Hom.:

14539

AF XY:

0.333

AC XY:

39986

AN XY:

120230

show subpopulations

Gnomad AFR exome

AF:

0.523

Gnomad AMR exome

AF:

0.420

Gnomad ASJ exome

AF:

0.292

Gnomad EAS exome

AF:

0.686

Gnomad SAS exome

AF:

0.350

Gnomad FIN exome

AF:

0.250

Gnomad NFE exome

AF:

0.252

Gnomad OTH exome

AF:

0.323

GnomAD4 exome

AF:

0.279

AC:

381740

AN:

1369548

Hom.:

59361

Cov.:

AF XY:

0.279

AC XY:

191052

AN XY:

684678

show subpopulations

Gnomad4 AFR exome

AF:

0.531

Gnomad4 AMR exome

AF:

0.413

Gnomad4 ASJ exome

AF:

0.292

Gnomad4 EAS exome

AF:

0.697

Gnomad4 SAS exome

AF:

0.341

Gnomad4 FIN exome

AF:

0.249

Gnomad4 NFE exome

AF:

0.244

Gnomad4 OTH exome

AF:

0.315

GnomAD4 genome

AF:

0.355

AC:

54019

AN:

152130

Hom.:

10926

Cov.:

AF XY:

0.357

AC XY:

26536

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.517

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.285

Gnomad4 EAS

AF:

0.689

Gnomad4 SAS

AF:

0.365

Gnomad4 FIN

AF:

0.240

Gnomad4 NFE

AF:

0.244

Gnomad4 OTH

AF:

0.379

Alfa

AF:

0.268

Hom.:

8016

Bravo

AF:

0.375

Asia WGS

AF:

0.540

AC:

1876

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.71

DANN

Benign

0.38

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over