Genetic Variant NM_001144936.2:c.93G>A (chr11-63768530-C-T) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7

The NM_001144936.2(ZFTA):c.93G>A(p.Pro31Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000255 in 1,185,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00024 ( 0 hom. )

Consequence

ZFTA
NM_001144936.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.879

Publications

0 publications found

Variant links:

Genes affected

ZFTA (HGNC:28449): (zinc finger translocation associated) Predicted to be involved in negative regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

ZFTA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BP6

Variant 11-63768530-C-T is Benign according to our data. Variant chr11-63768530-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2641903.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.879 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144936.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFTA	NM_001144936.2	MANE Select	c.93G>A	p.Pro31Pro	synonymous	Exon 1 of 5	NP_001138408.1	C9JLR9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZFTA	ENST00000433688.2	TSL:5 MANE Select	c.93G>A	p.Pro31Pro	synonymous	Exon 1 of 5	ENSP00000482180.1	C9JLR9
ZFTA	ENST00000948030.1		c.93G>A	p.Pro31Pro	synonymous	Exon 1 of 4	ENSP00000618089.1
ZFTA	ENST00000918477.1		c.93G>A	p.Pro31Pro	synonymous	Exon 1 of 4	ENSP00000588536.1

Frequencies

GnomAD3 genomes

AF:

0.000333

AC:

AN:

147222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000489

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000201

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000455

Gnomad OTH

AF:

0.000984

GnomAD2 exomes

AF:

0.00145

AC:

AN:

26830

AF XY:

0.00167

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000171

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000569

Gnomad OTH exome

AF:

0.00238

GnomAD4 exome

AF:

0.000244

AC:

253

AN:

1037798

Hom.:

Cov.:

AF XY:

0.000302

AC XY:

153

AN XY:

506354

show subpopulations

African (AFR)

AF:

0.0000517

AC:

AN:

19326

American (AMR)

AF:

0.0000960

AC:

AN:

10412

Ashkenazi Jewish (ASJ)

AF:

0.0111

AC:

126

AN:

11374

East Asian (EAS)

AF:

0.00

AC:

AN:

12928

South Asian (SAS)

AF:

0.000479

AC:

AN:

47982

European-Finnish (FIN)

AF:

0.00

AC:

AN:

15428

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2436

European-Non Finnish (NFE)

AF:

0.0000795

AC:

AN:

880968

Other (OTH)

AF:

0.000866

AC:

AN:

36944

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

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:

0.000333

AC:

AN:

147222

Hom.:

Cov.:

AF XY:

0.000251

AC XY:

AN XY:

71660

show subpopulations

African (AFR)

AF:

0.0000489

AC:

AN:

40876

American (AMR)

AF:

0.000201

AC:

AN:

14894

Ashkenazi Jewish (ASJ)

AF:

0.0112

AC:

AN:

3384

East Asian (EAS)

AF:

0.00

AC:

AN:

4990

South Asian (SAS)

AF:

0.000208

AC:

AN:

4800

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9076

Middle Eastern (MID)

AF:

0.00

AC:

AN:

314

European-Non Finnish (NFE)

AF:

0.0000455

AC:

AN:

65952

Other (OTH)

AF:

0.000984

AC:

AN:

2032

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.000214

Hom.:

Bravo

AF:

0.000404

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Uncertain

0.98

PhyloP100

-0.88

PromoterAI

0.038

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.0

Mutation Taster

=98/2

polymorphism

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over