19-23357415-T-C

Variant names:

• chr19-23357415-T-C
• rs1020075
• ENST00000593341.1:n.551+1015A>G

Variant summary

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

The ENST00000593341.1(ZNF91):​n.551+1015A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,156 control chromosomes in the GnomAD database, including 2,925 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 0.19 (2925 hom., cov: 33)
• Consequence: ZNF91 ENST00000593341.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 5 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF91	XM_024451693.2	c.254-15150A>G		intron_variant	Intron 3 of 3		XP_024307461.1
ZNF91	XR_001753754.3	n.4666+1015A>G		intron_variant	Intron 4 of 4
ZNF91	XR_007066978.1	n.4666+1015A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF91	ENST00000593341.1	n.551+1015A>G		intron_variant	Intron 1 of 1	1
ZNF91	ENST00000599743.5	c.253+16327A>G		intron_variant	Intron 3 of 3	3		ENSP00000468867.1
ZNF91	ENST00000596528.1	n.116+1315A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28642 AN: 152038 Hom.: 2920 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.188 AC: 28675 AN: 152156 Hom.: 2925 Cov.: 33 AF XY: 0.182 AC XY: 13533 AN XY: 74386

African (AFR) AF: 0.210 AC: 8701 AN: 41504

American (AMR) AF: 0.129 AC: 1965 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5182

South Asian (SAS) AF: 0.128 AC: 618 AN: 4832

European-Finnish (FIN) AF: 0.149 AC: 1581 AN: 10584

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14361 AN: 67980

Other (OTH) AF: 0.190 AC: 401 AN: 2110

Alfa AF: 0.204 Hom.: 9018

Bravo AF: 0.190

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		0.015
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1020075; hg19: chr19-23540217; COSMIC: COSV56091451; COSMIC: COSV56091451;