rs1079204

Positions:

• chr2-218265791-G-A
• chr2-218265791-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001087.5(AAMP):​c.879+40C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,589,694 control chromosomes in the GnomAD database, including 812 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.031 (79 hom., cov: 32)
  • Exomes 𝑓: 0.029 (733 hom.)
• Consequence: AAMP NM_001087.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

Genes affected

AAMP (HGNC:18): (angio associated migratory cell protein) The gene is a member of the immunoglobulin superfamily. The encoded protein is associated with angiogenesis, with potential roles in endothelial tube formation and the migration of endothelial cells. It may also regulate smooth muscle cell migration via the RhoA pathway. The encoded protein can bind to heparin and may mediate heparin-sensitive cell adhesion. [provided by RefSeq, Oct 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0312 (4758/152286) while in subpopulation AFR AF= 0.0346 (1436/41548). AF 95% confidence interval is 0.0331. There are 79 homozygotes in gnomad4. There are 2295 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 79 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AAMP	NM_001087.5	c.879+40C>T		intron_variant		ENST00000248450.9	NP_001078.2
AAMP	NM_001302545.2	c.882+40C>T		intron_variant			NP_001289474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AAMP	ENST00000248450.9	c.879+40C>T		intron_variant		1	NM_001087.5	ENSP00000248450	A1

Frequencies

GnomAD3 genomes AF: 0.0313 AC: 4756 AN: 152168 Hom.: 79 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0349

GnomAD3 exomes AF: 0.0267 AC: 6540 AN: 244588 Hom.: 93 AF XY: 0.0268 AC XY: 3549 AN XY: 132506

Gnomad AFR exome AF: 0.0341

Gnomad AMR exome AF: 0.0218

Gnomad ASJ exome AF: 0.0507

Gnomad EAS exome AF: 0.00252

Gnomad SAS exome AF: 0.0158

Gnomad FIN exome AF: 0.0225

Gnomad NFE exome AF: 0.0325

Gnomad OTH exome AF: 0.0339

GnomAD4 exome AF: 0.0295 AC: 42335 AN: 1437408 Hom.: 733 Cov.: 29 AF XY: 0.0294 AC XY: 21001 AN XY: 715168

Gnomad4 AFR exome AF: 0.0330

Gnomad4 AMR exome AF: 0.0226

Gnomad4 ASJ exome AF: 0.0486

Gnomad4 EAS exome AF: 0.00132

Gnomad4 SAS exome AF: 0.0169

Gnomad4 FIN exome AF: 0.0231

Gnomad4 NFE exome AF: 0.0315

Gnomad4 OTH exome AF: 0.0284

GnomAD4 genome AF: 0.0312 AC: 4758 AN: 152286 Hom.: 79 Cov.: 32 AF XY: 0.0308 AC XY: 2295 AN XY: 74454

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.0246

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0332

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0286 Hom.: 43

Bravo AF: 0.0317

Asia WGS AF: 0.0220 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.010
DANN	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs1079204; hg19: chr2-219130514;