chrX-8534047-G-A

Position:

• chrX-8534047-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000216.4(ANOS1):​c.1984+272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.078 (431 hom., 2351 hem., cov: 20)
• Consequence: ANOS1 NM_000216.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.451

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant X-8534047-G-A is Benign according to our data. Variant chrX-8534047-G-A is described in ClinVar as [Benign]. Clinvar id is 1273399.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANOS1	NM_000216.4	c.1984+272C>T		intron_variant		ENST00000262648.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANOS1	ENST00000262648.8	c.1984+272C>T		intron_variant		1	NM_000216.4	P1

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 8380 AN: 107662 Hom.: 428 Cov.: 20 AF XY: 0.0775 AC XY: 2345 AN XY: 30266

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.0975

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0819

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.0779 AC: 8392 AN: 107688 Hom.: 431 Cov.: 20 AF XY: 0.0776 AC XY: 2351 AN XY: 30304

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0770 Hom.: 429

Bravo AF: 0.0923

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.72

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

Other links and lift over

dbSNP: rs56051736; hg19: chrX-8502088;