Variant chr19-19320880-AGCGGCCCAGGCGGCG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2

The NM_015329.4(MAU2):c.33_47delGGCGGCGGCCCAGGC(p.Ala12_Ala16del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0133 in 1,516,008 control chromosomes in the GnomAD database, including 167 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0094 ( 16 hom., cov: 33)

Exomes 𝑓: 0.014 ( 151 hom. )

Consequence

MAU2
NM_015329.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.77

Variant links:

Genes affected

MAU2 (HGNC:29140): (MAU2 sister chromatid cohesion factor) Enables protein N-terminus binding activity. Involved in cohesin loading and maintenance of mitotic sister chromatid cohesion. Located in chromatin and nuclear body. Part of Scc2-Scc4 cohesin loading complex. [provided by Alliance of Genome Resources, Apr 2022]

MAU2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_015329.4.

BP6

Variant 19-19320880-AGCGGCCCAGGCGGCG-A is Benign according to our data. Variant chr19-19320880-AGCGGCCCAGGCGGCG-A is described in ClinVar as [Benign]. Clinvar id is 771929.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0137 (18710/1364568) while in subpopulation NFE AF= 0.0155 (16507/1065808). AF 95% confidence interval is 0.0153. There are 151 homozygotes in gnomad4_exome. There are 9160 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1420 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAU2	NM_015329.4 link	c.33_47delGGCGGCGGCCCAGGC	p.Ala12_Ala16del	disruptive_inframe_deletion	1/19	ENST00000262815.13	NP_056144.3	Q9Y6X3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAU2	ENST00000262815.13 link	c.33_47delGGCGGCGGCCCAGGC	p.Ala12_Ala16del	disruptive_inframe_deletion	1/19	1	NM_015329.4	ENSP00000262815.9		Q9Y6X3-1

Frequencies

GnomAD3 genomes

AF:

0.00938

AC:

1420

AN:

151326

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00271

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00910

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00354

Gnomad FIN

AF:

0.0130

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0141

Gnomad OTH

AF:

0.0121

GnomAD3 exomes

AF:

0.0121

AC:

1496

AN:

124134

Hom.:

AF XY:

0.0121

AC XY:

839

AN XY:

69120

show subpopulations

Gnomad AFR exome

AF:

0.00289

Gnomad AMR exome

AF:

0.0110

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00370

Gnomad FIN exome

AF:

0.0107

Gnomad NFE exome

AF:

0.0181

Gnomad OTH exome

AF:

0.0156

GnomAD4 exome

AF:

0.0137

AC:

18710

AN:

1364568

Hom.:

151

AF XY:

0.0136

AC XY:

9160

AN XY:

674068

show subpopulations

Gnomad4 AFR exome

AF:

0.00228

Gnomad4 AMR exome

AF:

0.0100

Gnomad4 ASJ exome

AF:

0.0108

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00356

Gnomad4 FIN exome

AF:

0.0108

Gnomad4 NFE exome

AF:

0.0155

Gnomad4 OTH exome

AF:

0.0136

GnomAD4 genome

AF:

0.00938

AC:

1420

AN:

151440

Hom.:

Cov.:

AF XY:

0.00902

AC XY:

668

AN XY:

74052

show subpopulations

Gnomad4 AFR

AF:

0.00270

Gnomad4 AMR

AF:

0.00909

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00354

Gnomad4 FIN

AF:

0.0130

Gnomad4 NFE

AF:

0.0141

Gnomad4 OTH

AF:

0.0119

Alfa

AF:

0.00189

Hom.:

Bravo

AF:

0.00931

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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