chr14-102922443-A-T

Variant names:

• chr14-102922443-A-T
• rs1211497
• NM_030943.4:c.-246A>T

Variant summary

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

The NM_030943.4(AMN):​c.-246A>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,028 control chromosomes in the GnomAD database, including 18,699 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (18699 hom., cov: 31)
• Consequence: AMN NM_030943.4 upstream_gene
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.62

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 14-102922443-A-T is Benign according to our data. Variant chr14-102922443-A-T is described in ClinVar as [Benign]. Clinvar id is 1231371.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMN	NM_030943.4	c.-246A>T		upstream_gene_variant		ENST00000299155.10	NP_112205.2
AMN	NM_001425246.1	c.-427A>T		upstream_gene_variant			NP_001412175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMN	ENST00000299155.10	c.-246A>T		upstream_gene_variant		1	NM_030943.4	ENSP00000299155.6

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69280 AN: 151910 Hom.: 18645 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.457 AC: 69402 AN: 152028 Hom.: 18699 Cov.: 31 AF XY: 0.457 AC XY: 33961 AN XY: 74328

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.442

Alfa AF: 0.393 Hom.: 1786

Bravo AF: 0.483

Asia WGS AF: 0.501 AC: 1738 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 07, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.13
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1211497; hg19: chr14-103388780;