Genetic Variant AMANZI:n.2422T>C (chr2-112842749-T-C) – 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.2422T>C 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 0.602 in 152,038 control chromosomes in the GnomAD database, including 28,021 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 0.60 ( 28007 hom., cov: 32)

Exomes 𝑓: 0.67 ( 14 hom. )

Consequence

AMANZI
ENST00000623243.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

11 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623243.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMANZI	NR_197592.1		n.2958T>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
AMANZI	ENST00000623243.1	TSL:6	n.2422T>C	non_coding_transcript_exon	Exon 1 of 1
ENSG00000299339	ENST00000762706.1		n.405-42509T>C	intron	N/A
ENSG00000299339	ENST00000762707.1		n.500-42509T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.602

AC:

91428

AN:

151860

Hom.:

27986

Cov.:

show subpopulations

Gnomad AFR

AF:

0.555

Gnomad AMI

AF:

0.736

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.652

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.596

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.667

Gnomad OTH

AF:

0.608

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

Cov.:

AF XY:

0.674

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.761

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.563

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.602

AC:

91480

AN:

151978

Hom.:

28007

Cov.:

AF XY:

0.593

AC XY:

44077

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.555

AC:

23010

AN:

41434

American (AMR)

AF:

0.509

AC:

7776

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.652

AC:

2260

AN:

3468

East Asian (EAS)

AF:

0.525

AC:

2711

AN:

5164

South Asian (SAS)

AF:

0.408

AC:

1966

AN:

4822

European-Finnish (FIN)

AF:

0.596

AC:

6284

AN:

10540

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.667

AC:

45332

AN:

67966

Other (OTH)

AF:

0.602

AC:

1271

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1844

3688

5532

7376

9220

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.632

Hom.:

3822

Bravo

AF:

0.597

Asia WGS

AF:

0.463

AC:

1609

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.15

(source)

DANN

Benign

0.57

PhyloP100

-1.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over