19-23335137-A-G

Variant names:

• chr19-23335137-A-G
• rs29984
• XR_007066978.1:n.8584T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000596528.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF91	ENST00000596528.1	TSL:2	n.116+23593T>C		intron	N/A
	ZNF91	ENST00000596989.1	TSL:3	n.371-26040T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78399 AN: 151904 Hom.: 21708 Cov.: 32

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.: 32 AF XY: 0.518 AC XY: 38449 AN XY: 74290

African (AFR) AF: 0.698 AC: 28969 AN: 41476

American (AMR) AF: 0.512 AC: 7835 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1531 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4330 AN: 5124

South Asian (SAS) AF: 0.507 AC: 2444 AN: 4824

European-Finnish (FIN) AF: 0.405 AC: 4276 AN: 10548

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27579 AN: 67976

Other (OTH) AF: 0.478 AC: 1009 AN: 2112

Alfa AF: 0.334 Hom.: 941

Bravo AF: 0.533

Asia WGS AF: 0.640 AC: 2229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.64
PhyloP100		-0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs29984; hg19: chr19-23517939; COSMIC: COSV74084436;