Variant chrX-8533991-AAAG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_000216.4(ANOS1):c.1984+325_1984+327del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.64 ( 16410 hom., 15999 hem., cov: 0)

Failed GnomAD Quality Control

Consequence

ANOS1
NM_000216.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.103

Variant links:

Genes affected

ANOS1 (HGNC:6211): (anosmin 1) Mutations in this gene cause the X-linked Kallmann syndrome. The encoded protein is similar in sequence to proteins known to function in neural cell adhesion and axonal migration. In addition, this cell surface protein is N-glycosylated and may have anti-protease activity. [provided by RefSeq, Jul 2008]

ANOS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant X-8533991-AAAG-A is Benign according to our data. Variant chrX-8533991-AAAG-A is described in ClinVar as [Benign]. Clinvar id is 1286210.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANOS1	NM_000216.4 linkuse as main transcript	c.1984+325_1984+327del		intron_variant		ENST00000262648.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANOS1	ENST00000262648.8 linkuse as main transcript	c.1984+325_1984+327del		intron_variant		1	NM_000216.4	P1

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

65735

AN:

103394

Hom.:

16417

Cov.:

AF XY:

0.597

AC XY:

16001

AN XY:

26824

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.561

Gnomad ASJ

AF:

0.692

Gnomad EAS

AF:

0.662

Gnomad SAS

AF:

0.482

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.701

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.648

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.635

AC:

65716

AN:

103413

Hom.:

16410

Cov.:

AF XY:

0.596

AC XY:

15999

AN XY:

26855

show subpopulations

Gnomad4 AFR

AF:

0.538

Gnomad4 AMR

AF:

0.560

Gnomad4 ASJ

AF:

0.692

Gnomad4 EAS

AF:

0.661

Gnomad4 SAS

AF:

0.480

Gnomad4 FIN

AF:

0.576

Gnomad4 NFE

AF:

0.712

Gnomad4 OTH

AF:

0.647

Alfa

AF:

0.682

Hom.:

4731

Asia WGS

AF:

0.571

AC:

1436

AN:

2514

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

Aug 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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