Variant rs1938596 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_053023.5(ZFP91):c.988-16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 1,502,596 control chromosomes in the GnomAD database, including 145,799 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 0.49 ( 19218 hom., cov: 30)

Exomes 𝑓: 0.43 ( 126581 hom. )

Consequence

ZFP91
NM_053023.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

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:

ZFP91-CNTF (HGNC:):

ZFP91-CNTF links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
ZFP91	NM_053023.5 linkuse as main transcript	c.988-16A>G	intron_variant	ENST00000316059.7	NP_444251.1
ZFP91	NM_001197051.2 linkuse as main transcript	c.985-16A>G	intron_variant		NP_001183980.1
ZFP91-CNTF	NR_024091.1 linkuse as main transcript	n.1156-16A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ZFP91	ENST00000316059.7 linkuse as main transcript	c.988-16A>G	intron_variant	1	NM_053023.5	ENSP00000339030.5	Q96JP5-1
ZFP91-CNTF	ENST00000389919.8 linkuse as main transcript	n.988-16A>G	intron_variant	2		ENSP00000455911.1	A0A0A6YYC7
ZFP91-CNTF	ENST00000422974.2 linkuse as main transcript	n.469-16A>G	intron_variant	5		ENSP00000457288.1	H3BTR0

Frequencies

GnomAD3 genomes

AF:

0.493

AC:

74516

AN:

151060

Hom.:

19184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.421

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.474

GnomAD3 exomes

AF:

0.444

AC:

91526

AN:

206086

Hom.:

21292

AF XY:

0.444

AC XY:

49783

AN XY:

112248

show subpopulations

Gnomad AFR exome

AF:

0.657

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.407

Gnomad EAS exome

AF:

0.321

Gnomad SAS exome

AF:

0.464

Gnomad FIN exome

AF:

0.518

Gnomad NFE exome

AF:

0.432

Gnomad OTH exome

AF:

0.434

GnomAD4 exome

AF:

0.429

AC:

579128

AN:

1351420

Hom.:

126581

Cov.:

AF XY:

0.429

AC XY:

286804

AN XY:

667792

show subpopulations

Gnomad4 AFR exome

AF:

0.666

Gnomad4 AMR exome

AF:

0.385

Gnomad4 ASJ exome

AF:

0.410

Gnomad4 EAS exome

AF:

0.355

Gnomad4 SAS exome

AF:

0.463

Gnomad4 FIN exome

AF:

0.510

Gnomad4 NFE exome

AF:

0.420

Gnomad4 OTH exome

AF:

0.429

GnomAD4 genome

AF:

0.493

AC:

74598

AN:

151176

Hom.:

19218

Cov.:

AF XY:

0.495

AC XY:

36552

AN XY:

73784

show subpopulations

Gnomad4 AFR

AF:

0.655

Gnomad4 AMR

AF:

0.432

Gnomad4 ASJ

AF:

0.420

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.466

Gnomad4 FIN

AF:

0.522

Gnomad4 NFE

AF:

0.424

Gnomad4 OTH

AF:

0.471

Alfa

AF:

0.451

Hom.:

3735

Bravo

AF:

0.490

Asia WGS

AF:

0.409

AC:

1420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.087

DANN

Benign

0.14

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over