11-58579480-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_053023.5(ZFP91):c.199G>A(p.Ala67Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00868 in 1,506,646 control chromosomes in the GnomAD database, including 75 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A67G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0062 ( 7 hom., cov: 31)

Exomes 𝑓: 0.0090 ( 68 hom. )

Consequence

ZFP91
NM_053023.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.26

Publications

3 publications found

Variant links:

Genes affected

ZFP91 (HGNC:14983): (ZFP91 zinc finger protein, atypical E3 ubiquitin ligase) The protein encoded by this gene is a member of the zinc finger family of proteins. The gene product contains C2H2-type domains, which are the classical zinc finger domains found in numerous nucleic acid-binding proteins. This protein functions as a regulator of the non-canonical NF-kappaB pathway in lymphotoxin-beta receptor signaling. Alternative splicing results in multiple transcript variants. A read-through transcript variant composed of ZFP91 and the downstream CNTF gene sequence has been identified, but it is thought to be non-coding. Read-through transcription of ZFP91 and CNTF has also been observed in mouse. A ZFP91-related pseudogene has also been identified on chromosome 2. [provided by RefSeq, Oct 2010]

ZFP91 links:

ZFP91-CNTF (HGNC:33441): (ZFP91-CNTF readthrough (NMD candidate)) This gene represents a read-through transcript composed of ZFP91 and CNTF sequence. This transcript is thought to be non-coding because it would be subject to nonsense-mediated mRNA decay (NMD). Read-through transcription of ZFP91 and CNTF has also been observed in mouse. [provided by RefSeq, Aug 2008]

ZFP91-CNTF links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005238235).

BS2

High Homozygotes in GnomAd4 at 7 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053023.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZFP91	NM_053023.5	MANE Select	c.199G>A	p.Ala67Thr	missense	Exon 1 of 11	NP_444251.1	Q96JP5-1
ZFP91	NM_001197051.2		c.199G>A	p.Ala67Thr	missense	Exon 1 of 11	NP_001183980.1
ZFP91-CNTF	NR_024091.1		n.367G>A		non_coding_transcript_exon	Exon 1 of 13

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZFP91	ENST00000316059.7	TSL:1 MANE Select	c.199G>A	p.Ala67Thr	missense	Exon 1 of 11	ENSP00000339030.5	Q96JP5-1
ZFP91-CNTF	ENST00000389919.8	TSL:2	n.199G>A		non_coding_transcript_exon	Exon 1 of 13	ENSP00000455911.1
ZFP91	ENST00000870367.1		c.199G>A	p.Ala67Thr	missense	Exon 2 of 12	ENSP00000540426.1

Frequencies

GnomAD3 genomes

AF:

0.00625

AC:

950

AN:

152002

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00172

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00275

Gnomad ASJ

AF:

0.00662

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.00904

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00918

Gnomad OTH

AF:

0.00478

GnomAD2 exomes

AF:

0.00815

AC:

825

AN:

101220

AF XY:

0.00857

show subpopulations

Gnomad AFR exome

AF:

0.00469

Gnomad AMR exome

AF:

0.00338

Gnomad ASJ exome

AF:

0.00733

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00920

Gnomad NFE exome

AF:

0.00873

Gnomad OTH exome

AF:

0.00661

GnomAD4 exome

AF:

0.00896

AC:

12136

AN:

1354534

Hom.:

Cov.:

AF XY:

0.00913

AC XY:

6100

AN XY:

668236

show subpopulations

African (AFR)

AF:

0.00138

AC:

AN:

27454

American (AMR)

AF:

0.00322

AC:

AN:

30778

Ashkenazi Jewish (ASJ)

AF:

0.00732

AC:

172

AN:

23496

East Asian (EAS)

AF:

0.00

AC:

AN:

30710

South Asian (SAS)

AF:

0.0148

AC:

1126

AN:

75992

European-Finnish (FIN)

AF:

0.00809

AC:

330

AN:

40796

Middle Eastern (MID)

AF:

0.00164

AC:

AN:

4260

European-Non Finnish (NFE)

AF:

0.00927

AC:

9872

AN:

1064896

Other (OTH)

AF:

0.00876

AC:

492

AN:

56152

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

791

1582

2374

3165

3956

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.00624

AC:

949

AN:

152112

Hom.:

Cov.:

AF XY:

0.00659

AC XY:

490

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.00171

AC:

AN:

41518

American (AMR)

AF:

0.00268

AC:

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00662

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5112

South Asian (SAS)

AF:

0.0172

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00904

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00918

AC:

624

AN:

67950

Other (OTH)

AF:

0.00473

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

146

195

244

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00534

Hom.:

Bravo

AF:

0.00512

ESP6500AA

AF:

0.000877

AC:

ESP6500EA

AF:

0.00748

AC:

ExAC

AF:

0.00463

AC:

466

Asia WGS

AF:

0.00376

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.50

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.058

Eigen

Uncertain

0.19

Eigen_PC

Benign

0.17

FATHMM_MKL

Benign

0.75

LIST_S2

Benign

0.57

MetaRNN

Benign

0.0052

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.55

PhyloP100

4.3

PrimateAI

Pathogenic

0.93

PROVEAN

Benign

0.18

REVEL

Benign

0.12

Sift

Pathogenic

0.0

Sift4G

Benign

0.86

Polyphen

0.98

Vest4

0.33

MVP

0.082

MPC

0.21

ClinPred

0.11

GERP RS

3.7

PromoterAI

0.026

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.8

Varity_R

0.30

gMVP

0.15

Mutation Taster

=99/1

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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