19-24058103-C-T

Variant names:

• chr19-24058103-C-T
• rs17304569
• ENST00000652968.1:n.587C>T

Variant summary

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

The ENST00000652968.1(ENSG00000268362):​n.587C>T 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 0.156 in 152,120 control chromosomes in the GnomAD database, including 1,869 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 0.16 (1869 hom., cov: 32)
• Consequence: ENSG00000268362 ENST00000652968.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 1 publications found

Genes affected

ENSG00000268362 (HGNC:):

ZNF254 (HGNC:13047): (zinc finger protein 254) Zinc finger proteins have been shown to interact with nucleic acids and to have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form 1 family of zinc finger proteins. See ZFP93 (MIM 604749) for additional information on zinc finger proteins.[supplied by OMIM, Jul 2002]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF254	XM_047439738.1	c.-1936C>T		5_prime_UTR_variant	Exon 4 of 9		XP_047295694.1
ZNF254	XM_047439739.1	c.-1810C>T		5_prime_UTR_variant	Exon 4 of 8		XP_047295695.1
ZNF254	XM_047439742.1	c.-1810C>T		5_prime_UTR_variant	Exon 5 of 9		XP_047295698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268362	ENST00000652968.1	n.587C>T		non_coding_transcript_exon_variant	Exon 4 of 6
ENSG00000268362	ENST00000653003.1	n.620C>T		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000268362	ENST00000653308.1	n.645C>T		non_coding_transcript_exon_variant	Exon 5 of 7

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23726 AN: 151998 Hom.: 1864 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.156 AC: 23750 AN: 152120 Hom.: 1869 Cov.: 32 AF XY: 0.155 AC XY: 11536 AN XY: 74372

African (AFR) AF: 0.160 AC: 6647 AN: 41506

American (AMR) AF: 0.110 AC: 1686 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3472

East Asian (EAS) AF: 0.174 AC: 896 AN: 5152

South Asian (SAS) AF: 0.152 AC: 735 AN: 4822

European-Finnish (FIN) AF: 0.183 AC: 1936 AN: 10574

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10959 AN: 68000

Other (OTH) AF: 0.134 AC: 283 AN: 2108

Alfa AF: 0.155 Hom.: 685

Bravo AF: 0.152

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.19
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: rs17304569; hg19: chr19-24240905;