dbSNP rs1079204: AAMP:c.879+40C>T (chr2-218265791-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.743

Publications

11 publications found

Variant links:

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]

AAMP links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 79 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AAMP	NM_001087.5 link	c.879+40C>T		intron_variant	Intron 7 of 10	ENST00000248450.9	NP_001078.2
AAMP	NM_001302545.2 link	c.882+40C>T		intron_variant	Intron 7 of 10		NP_001289474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AAMP	ENST00000248450.9 link	c.879+40C>T		intron_variant	Intron 7 of 10	1	NM_001087.5	ENSP00000248450.4

Frequencies

GnomAD3 genomes

AF:

0.0313

AC:

4756

AN:

152168

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.0267

AC:

6540

AN:

244588

AF XY:

0.0268

show subpopulations

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 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.:

AF XY:

0.0294

AC XY:

21001

AN XY:

715168

show subpopulations

African (AFR)

AF:

0.0330

AC:

1089

AN:

33016

American (AMR)

AF:

0.0226

AC:

1004

AN:

44402

Ashkenazi Jewish (ASJ)

AF:

0.0486

AC:

1251

AN:

25736

East Asian (EAS)

AF:

0.00132

AC:

AN:

39432

South Asian (SAS)

AF:

0.0169

AC:

1447

AN:

85486

European-Finnish (FIN)

AF:

0.0231

AC:

1186

AN:

51410

Middle Eastern (MID)

AF:

0.0407

AC:

233

AN:

5720

European-Non Finnish (NFE)

AF:

0.0315

AC:

34379

AN:

1092654

Other (OTH)

AF:

0.0284

AC:

1694

AN:

59552

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

2197

4394

6592

8789

10986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1276

2552

3828

5104

6380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0312

AC:

4758

AN:

152286

Hom.:

Cov.:

AF XY:

0.0308

AC XY:

2295

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.0346

AC:

1436

AN:

41548

American (AMR)

AF:

0.0246

AC:

377

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0582

AC:

202

AN:

3472

East Asian (EAS)

AF:

0.00386

AC:

AN:

5182

South Asian (SAS)

AF:

0.0145

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0262

AC:

278

AN:

10622

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0332

AC:

2260

AN:

68024

Other (OTH)

AF:

0.0341

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

250

500

750

1000

1250

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0305

Hom.:

Bravo

AF:

0.0317

Asia WGS

AF:

0.0220

AC:

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

(source)

DANN

Benign

0.60

PhyloP100

-0.74

PromoterAI

-0.0072

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over