Variant 14-102922662-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The 14-102922662-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 1,590,276 control chromosomes in the GnomAD database, including 180,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.47 ( 17105 hom., cov: 31)

Exomes 𝑓: 0.47 ( 163358 hom. )

Consequence

AMN
NM_030943.4 upstream_gene

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.15

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 -14 ACMG points.

BP4

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

BP6

Variant 14-102922662-T-C is Benign according to our data. Variant chr14-102922662-T-C is described in ClinVar as [Benign]. Clinvar id is 1243841.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AMN	NM_030943.4 linkuse as main transcript			upstream_gene_variant		ENST00000299155.10
AMN	XM_011537202.4 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMN	ENST00000299155.10 linkuse as main transcript			upstream_gene_variant		1	NM_030943.4	P1	Q9BXJ7-1

Frequencies

GnomAD3 genomes

AF:

0.471

AC:

71397

AN:

151614

Hom.:

17085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.369

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.475

GnomAD3 exomes

AF:

0.440

AC:

94665

AN:

215196

Hom.:

21415

AF XY:

0.436

AC XY:

50933

AN XY:

116826

show subpopulations

Gnomad AFR exome

AF:

0.453

Gnomad AMR exome

AF:

0.503

Gnomad ASJ exome

AF:

0.501

Gnomad EAS exome

AF:

0.192

Gnomad SAS exome

AF:

0.370

Gnomad FIN exome

AF:

0.427

Gnomad NFE exome

AF:

0.476

Gnomad OTH exome

AF:

0.461

GnomAD4 exome

AF:

0.473

AC:

680874

AN:

1438544

Hom.:

163358

Cov.:

AF XY:

0.470

AC XY:

335748

AN XY:

713938

show subpopulations

Gnomad4 AFR exome

AF:

0.459

Gnomad4 AMR exome

AF:

0.507

Gnomad4 ASJ exome

AF:

0.505

Gnomad4 EAS exome

AF:

0.237

Gnomad4 SAS exome

AF:

0.380

Gnomad4 FIN exome

AF:

0.450

Gnomad4 NFE exome

AF:

0.488

Gnomad4 OTH exome

AF:

0.466

GnomAD4 genome

AF:

0.471

AC:

71462

AN:

151732

Hom.:

17105

Cov.:

AF XY:

0.469

AC XY:

34772

AN XY:

74130

show subpopulations

Gnomad4 AFR

AF:

0.470

Gnomad4 AMR

AF:

0.510

Gnomad4 ASJ

AF:

0.495

Gnomad4 EAS

AF:

0.213

Gnomad4 SAS

AF:

0.369

Gnomad4 FIN

AF:

0.458

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.471

Alfa

AF:

0.427

Hom.:

2941

Bravo

AF:

0.478

Asia WGS

AF:

0.346

AC:

1203

AN:

3478

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

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.086

DANN

Benign

0.48

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