Variant 14-102930718-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.*38G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 1,545,532 control chromosomes in the GnomAD database, including 353,428 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 32317 hom., cov: 35)

Exomes 𝑓: 0.68 ( 321111 hom. )

Consequence

AMN
NM_030943.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.447

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:

AMN (HGNC:):

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=-0.9).

BP6

Variant 14-102930718-G-C is Benign according to our data. Variant chr14-102930718-G-C is described in ClinVar as [Benign]. Clinvar id is 1245489.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
AMN	NM_030943.4 linkuse as main transcript	c.*38G>C	3_prime_UTR_variant	12/12	ENST00000299155.10	NP_112205.2	Q9BXJ7-1
AMN	XM_011537202.4 linkuse as main transcript	c.*38G>C	3_prime_UTR_variant	12/12			B3KP64
AMN	XM_011537203.4 linkuse as main transcript	c.*38G>C	3_prime_UTR_variant	12/12		XP_011535505.1	B3KP64

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AMN	ENST00000299155.10 linkuse as main transcript	c.*38G>C	3_prime_UTR_variant	12/12	1	NM_030943.4	ENSP00000299155.6	Q9BXJ7-1
AMN	ENST00000541086.5 linkuse as main transcript	n.2146G>C	non_coding_transcript_exon_variant	11/11	2
AMN	ENST00000558590.1 linkuse as main transcript	n.1220+225G>C	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98587

AN:

152072

Hom.:

32297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.566

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.699

Gnomad SAS

AF:

0.735

Gnomad FIN

AF:

0.630

Gnomad MID

AF:

0.759

Gnomad NFE

AF:

0.676

Gnomad OTH

AF:

0.671

GnomAD3 exomes

AF:

0.681

AC:

101731

AN:

149292

Hom.:

34730

AF XY:

0.686

AC XY:

55428

AN XY:

80784

show subpopulations

Gnomad AFR exome

AF:

0.570

Gnomad AMR exome

AF:

0.695

Gnomad ASJ exome

AF:

0.624

Gnomad EAS exome

AF:

0.687

Gnomad SAS exome

AF:

0.742

Gnomad FIN exome

AF:

0.645

Gnomad NFE exome

AF:

0.680

Gnomad OTH exome

AF:

0.702

GnomAD4 exome

AF:

0.678

AC:

944785

AN:

1393342

Hom.:

321111

Cov.:

AF XY:

0.680

AC XY:

467846

AN XY:

688328

show subpopulations

Gnomad4 AFR exome

AF:

0.564

Gnomad4 AMR exome

AF:

0.698

Gnomad4 ASJ exome

AF:

0.627

Gnomad4 EAS exome

AF:

0.708

Gnomad4 SAS exome

AF:

0.739

Gnomad4 FIN exome

AF:

0.647

Gnomad4 NFE exome

AF:

0.678

Gnomad4 OTH exome

AF:

0.675

GnomAD4 genome

AF:

0.648

AC:

98662

AN:

152190

Hom.:

32317

Cov.:

AF XY:

0.652

AC XY:

48538

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.566

Gnomad4 AMR

AF:

0.712

Gnomad4 ASJ

AF:

0.638

Gnomad4 EAS

AF:

0.700

Gnomad4 SAS

AF:

0.736

Gnomad4 FIN

AF:

0.630

Gnomad4 NFE

AF:

0.676

Gnomad4 OTH

AF:

0.672

Alfa

AF:

0.606

Hom.:

3544

Bravo

AF:

0.649

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 07, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.27

DANN

Benign

0.64

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