Genetic Variant AMANZI:n.351C>T (chr2-112840678-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

The ENST00000623243.1(AMANZI):n.351C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,140 control chromosomes in the GnomAD database, including 5,486 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 0.25 ( 5485 hom., cov: 32)

Exomes 𝑓: 0.17 ( 1 hom. )

Consequence

AMANZI
ENST00000623243.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

Publications

25 publications found

Variant links:

COSMIC-nc: COSV54521330

Genes affected

AMANZI (HGNC:55634):

AMANZI links:

ENSG00000299339 (HGNC:):

ENSG00000299339 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMANZI	NR_197592.1 link	n.887C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AMANZI	ENST00000623243.1 link	n.351C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000299339	ENST00000762706.1 link	n.405-44580C>T	intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1 link	n.500-44580C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37671

AN:

151976

Hom.:

5465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.398

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.396

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.245

GnomAD4 exome

AF:

0.174

AC:

AN:

Hom.:

Cov.:

AF XY:

0.192

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.227

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.100

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.248

AC:

37714

AN:

152094

Hom.:

5485

Cov.:

AF XY:

0.257

AC XY:

19098

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.108

AC:

4464

AN:

41520

American (AMR)

AF:

0.399

AC:

6099

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

760

AN:

3466

East Asian (EAS)

AF:

0.396

AC:

2048

AN:

5174

South Asian (SAS)

AF:

0.355

AC:

1712

AN:

4822

European-Finnish (FIN)

AF:

0.334

AC:

3515

AN:

10534

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.269

AC:

18304

AN:

67990

Other (OTH)

AF:

0.252

AC:

531

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1370

2739

4109

5478

6848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.261

Hom.:

9911

Bravo

AF:

0.246

Asia WGS

AF:

0.369

AC:

1284

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.27

(source)

DANN

Benign

0.55

PhyloP100

-1.8

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over