14-102930107-CCGCCCCGCCGCGCCT-CCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCT

Variant names:

• chr14-102930107-C-CCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCT
• rs386834161
• NM_030943.4:c.1007-31_1007-30insCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_030943.4(AMN):​c.1007-31_1007-30insCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: AMN NM_030943.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• Imerslund-Grasbeck syndrome type 1

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• Imerslund-Grasbeck syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030943.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMN	NM_030943.4	MANE Select	c.1007-31_1007-30insCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCG		intron	N/A	NP_112205.2	Q9BXJ7-1
	AMN	NM_001425246.1		c.845-31_845-30insCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCG		intron	N/A	NP_001412175.1	B3KP64

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMN	ENST00000299155.10	TSL:1 MANE Select	c.1007-31_1007-30insCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCG		intron	N/A	ENSP00000299155.6	Q9BXJ7-1
	AMN	ENST00000872999.1		c.950-31_950-30insCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCG		intron	N/A	ENSP00000543058.1
	AMN	ENST00000559789.1	TSL:3	c.125-31_125-30insCCTCGCCCCGCCGCGCCTCGCCCCGCCGCGCCTCGCCCCGCCGCG		intron	N/A	ENSP00000452831.1	H0YKJ5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs386834161; hg19: chr14-103396444;