Variant chr15-56429208-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_018365.4(MNS1):c.1396-15G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.999 in 1,538,092 control chromosomes in the GnomAD database, including 767,697 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 1.0 ( 75512 hom., cov: 31)

Exomes 𝑓: 1.0 ( 692185 hom. )

Consequence

MNS1
NM_018365.4 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0980

Variant links:

Genes affected

TEX9 (HGNC:29585): (testis expressed 9)

TEX9 links:

MNS1 (HGNC:29636): (meiosis specific nuclear structural 1) This gene encodes a protein highly similar to the mouse meiosis-specific nuclear structural 1 protein. The mouse protein was shown to be expressed at the pachytene stage during spermatogenesis and may function as a nuclear skeletal protein to regulate nuclear morphology during meiosis. [provided by RefSeq, Oct 2008]

MNS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 15-56429208-C-T is Benign according to our data. Variant chr15-56429208-C-T is described in ClinVar as [Benign]. Clinvar id is 1235571.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX9	NM_001395496.1 linkuse as main transcript	c.*764C>T		3_prime_UTR_variant	12/12	ENST00000696102.1
MNS1	NM_018365.4 linkuse as main transcript	c.1396-15G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000260453.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX9	ENST00000696102.1 linkuse as main transcript	c.*764C>T		3_prime_UTR_variant	12/12		NM_001395496.1	P1	Q8N6V9-1
MNS1	ENST00000260453.4 linkuse as main transcript	c.1396-15G>A		splice_polypyrimidine_tract_variant, intron_variant		1	NM_018365.4	P1

Frequencies

GnomAD3 genomes

AF:

0.996

AC:

151499

AN:

152090

Hom.:

75455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.987

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.998

Gnomad ASJ

AF:

0.997

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.997

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.996

GnomAD3 exomes

AF:

0.999

AC:

219154

AN:

219408

Hom.:

109453

AF XY:

0.999

AC XY:

119286

AN XY:

119396

show subpopulations

Gnomad AFR exome

AF:

0.988

Gnomad AMR exome

AF:

0.999

Gnomad ASJ exome

AF:

0.997

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

1.00

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

1.00

Gnomad OTH exome

AF:

0.998

GnomAD4 exome

AF:

0.999

AC:

1385127

AN:

1385884

Hom.:

692185

Cov.:

AF XY:

0.999

AC XY:

691424

AN XY:

691802

show subpopulations

Gnomad4 AFR exome

AF:

0.988

Gnomad4 AMR exome

AF:

0.999

Gnomad4 ASJ exome

AF:

0.998

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.999

GnomAD4 genome

AF:

0.996

AC:

151615

AN:

152208

Hom.:

75512

Cov.:

AF XY:

0.996

AC XY:

74133

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.987

Gnomad4 AMR

AF:

0.998

Gnomad4 ASJ

AF:

0.997

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

1.00

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

1.00

Gnomad4 OTH

AF:

0.996

Alfa

AF:

1.00

Hom.:

62234

Bravo

AF:

0.996

Asia WGS

AF:

1.00

AC:

3461

AN:

3462

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

GeneDx

Oct 30, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.56

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

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