Genetic Variant ENST00000623243.1:n.2511C>T (chr2-112842838-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000623243.1(AMANZI):n.2511C>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 0.379 in 152,124 control chromosomes in the GnomAD database, including 11,611 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 0.38 ( 11608 hom., cov: 32)

Exomes 𝑓: 0.35 ( 3 hom. )

Consequence

AMANZI
ENST00000623243.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.100

Publications

26 publications found

Variant links:

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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMANZI	NR_197592.1 link	n.3047C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AMANZI	ENST00000623243.1 link	n.2511C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000299339	ENST00000762706.1 link	n.405-42420C>T	intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1 link	n.500-42420C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57661

AN:

151946

Hom.:

11613

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.425

Gnomad AMR

AF:

0.348

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.475

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.389

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.387

GnomAD4 exome

AF:

0.350

AC:

AN:

Hom.:

Cov.:

AF XY:

0.345

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.375

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.375

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.379

AC:

57656

AN:

152064

Hom.:

11608

Cov.:

AF XY:

0.376

AC XY:

27963

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.259

AC:

10725

AN:

41480

American (AMR)

AF:

0.347

AC:

5304

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.399

AC:

1387

AN:

3472

East Asian (EAS)

AF:

0.475

AC:

2455

AN:

5168

South Asian (SAS)

AF:

0.277

AC:

1336

AN:

4828

European-Finnish (FIN)

AF:

0.389

AC:

4113

AN:

10570

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.457

AC:

31036

AN:

67944

Other (OTH)

AF:

0.382

AC:

808

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1791

3583

5374

7166

8957

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

548

1096

1644

2192

2740

<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:

0.389

Hom.:

2303

Bravo

AF:

0.375

Asia WGS

AF:

0.330

AC:

1145

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.2

(source)

DANN

Benign

0.53

PhyloP100

-0.10

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over