Variant 14-102922877-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_030943.4(AMN):c.43+146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 1,149,760 control chromosomes in the GnomAD database, including 3,266 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.058 ( 314 hom., cov: 33)

Exomes 𝑓: 0.072 ( 2952 hom. )

Consequence

AMN
NM_030943.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.39

Variant links:

Genes affected

AMN (HGNC:14604): (amnion associated transmembrane protein) The protein encoded by this gene is a type I transmembrane protein. It is thought to modulate bone morphogenetic protein (BMP) receptor function by serving as an accessory or coreceptor, and thus facilitates or hinders BMP binding. It is known that the mouse AMN gene is expressed in the extraembryonic visceral endoderm layer during gastrulation, but it is found to be mutated in amnionless mouse. The encoded protein has sequence similarity to short gastrulation (Sog) and procollagen IIA proteins in Drosophila. [provided by RefSeq, Jul 2008]

AMN 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=-0.79).

BP6

Variant 14-102922877-C-T is Benign according to our data. Variant chr14-102922877-C-T is described in ClinVar as [Benign]. Clinvar id is 1268789.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMN	NM_030943.4 linkuse as main transcript	c.43+146C>T		intron_variant		ENST00000299155.10	NP_112205.2
AMN	XM_011537202.4 linkuse as main transcript	c.-120+127C>T		intron_variant			XP_011535504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMN	ENST00000299155.10 linkuse as main transcript	c.43+146C>T		intron_variant		1	NM_030943.4	ENSP00000299155	P1	Q9BXJ7-1
AMN	ENST00000541086.5 linkuse as main transcript			upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0578

AC:

8795

AN:

152170

Hom.:

314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0304

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0434

Gnomad ASJ

AF:

0.0599

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.0429

Gnomad FIN

AF:

0.0617

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0731

Gnomad OTH

AF:

0.0516

GnomAD4 exome

AF:

0.0724

AC:

72221

AN:

997472

Hom.:

2952

Cov.:

AF XY:

0.0710

AC XY:

35104

AN XY:

494376

show subpopulations

Gnomad4 AFR exome

AF:

0.0257

Gnomad4 AMR exome

AF:

0.0309

Gnomad4 ASJ exome

AF:

0.0660

Gnomad4 EAS exome

AF:

0.159

Gnomad4 SAS exome

AF:

0.0440

Gnomad4 FIN exome

AF:

0.0702

Gnomad4 NFE exome

AF:

0.0748

Gnomad4 OTH exome

AF:

0.0656

GnomAD4 genome

AF:

0.0578

AC:

8798

AN:

152288

Hom.:

314

Cov.:

AF XY:

0.0590

AC XY:

4397

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.0304

Gnomad4 AMR

AF:

0.0434

Gnomad4 ASJ

AF:

0.0599

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.0431

Gnomad4 FIN

AF:

0.0617

Gnomad4 NFE

AF:

0.0731

Gnomad4 OTH

AF:

0.0516

Alfa

AF:

0.0639

Hom.:

Bravo

AF:

0.0565

Asia WGS

AF:

0.0730

AC:

254

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	Jul 31, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.80

DANN

Benign

0.43

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