Variant chr14-102922666-G-C 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.-23G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,592,304 control chromosomes in the GnomAD database, including 123,872 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14519 hom., cov: 32)

Exomes 𝑓: 0.38 ( 109353 hom. )

Consequence

AMN
NM_030943.4 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.64

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 14-102922666-G-C is Benign according to our data. Variant chr14-102922666-G-C is described in ClinVar as [Benign]. Clinvar id is 1262486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AMN	NM_030943.4 linkuse as main transcript	c.-23G>C		5_prime_UTR_variant	1/12	ENST00000299155.10
AMN	XM_011537202.4 linkuse as main transcript	c.-204G>C		5_prime_UTR_variant	1/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMN	ENST00000299155.10 linkuse as main transcript	c.-23G>C		5_prime_UTR_variant	1/12	1	NM_030943.4	P1	Q9BXJ7-1

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

64384

AN:

151722

Hom.:

14493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.440

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.366

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.400

GnomAD3 exomes

AF:

0.343

AC:

74710

AN:

217602

Hom.:

13681

AF XY:

0.342

AC XY:

40370

AN XY:

118152

show subpopulations

Gnomad AFR exome

AF:

0.555

Gnomad AMR exome

AF:

0.308

Gnomad ASJ exome

AF:

0.375

Gnomad EAS exome

AF:

0.0940

Gnomad SAS exome

AF:

0.286

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.383

Gnomad OTH exome

AF:

0.370

GnomAD4 exome

AF:

0.384

AC:

553364

AN:

1440464

Hom.:

109353

Cov.:

AF XY:

0.381

AC XY:

272199

AN XY:

714976

show subpopulations

Gnomad4 AFR exome

AF:

0.569

Gnomad4 AMR exome

AF:

0.320

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

0.111

Gnomad4 SAS exome

AF:

0.296

Gnomad4 FIN exome

AF:

0.356

Gnomad4 NFE exome

AF:

0.399

Gnomad4 OTH exome

AF:

0.384

GnomAD4 genome

AF:

0.425

AC:

64469

AN:

151840

Hom.:

14519

Cov.:

AF XY:

0.419

AC XY:

31068

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.564

Gnomad4 AMR

AF:

0.382

Gnomad4 ASJ

AF:

0.369

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.399

Gnomad4 OTH

AF:

0.397

Alfa

AF:

0.296

Hom.:

993

Bravo

AF:

0.434

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 15, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.4

DANN

Benign

0.55

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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