Variant 19-23335137-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_007066978.1(ZNF91):n.8584T>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 0.516 in 152,022 control chromosomes in the GnomAD database, including 21,764 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 0.52 ( 21764 hom., cov: 32)

Consequence

ZNF91
XR_007066978.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.888

Variant links:

Genes affected

ZNF91 (HGNC:13166): (zinc finger protein 91) The ZNF91 gene encodes a zinc finger protein of the KRAB (Kruppel-associated box) subfamily (Bellefroid et al., 1991, 1993 [PubMed 2023909] [PubMed 8467795]).[supplied by OMIM, May 2010]

ZNF91 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
ZNF91	XR_007066978.1 linkuse as main transcript	n.8584T>C	non_coding_transcript_exon_variant	5/7
ZNF91	XR_007066982.1 linkuse as main transcript	n.8488T>C	non_coding_transcript_exon_variant	4/6
ZNF91	XR_001753754.3 linkuse as main transcript	n.4666+23293T>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF91	ENST00000596528.1 linkuse as main transcript	n.116+23593T>C		intron_variant, non_coding_transcript_variant		2
ZNF91	ENST00000596989.1 linkuse as main transcript	n.371-26040T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78399

AN:

151904

Hom.:

21708

Cov.:

show subpopulations

Gnomad AFR

AF:

0.698

Gnomad AMI

AF:

0.461

Gnomad AMR

AF:

0.512

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.845

Gnomad SAS

AF:

0.507

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.474

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.516

AC:

78514

AN:

152022

Hom.:

21764

Cov.:

AF XY:

0.518

AC XY:

38449

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.698

Gnomad4 AMR

AF:

0.512

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.845

Gnomad4 SAS

AF:

0.507

Gnomad4 FIN

AF:

0.405

Gnomad4 NFE

AF:

0.406

Gnomad4 OTH

AF:

0.478

Alfa

AF:

0.310

Hom.:

771

Bravo

AF:

0.533

Asia WGS

AF:

0.640

AC:

2229

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.2

DANN

Benign

0.64

Splicing

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