19-2857289-A-C

Variant names:

• chr19-2857289-A-C
• rs4807347
• NM_152791.5:c.*3337A>C

Variant summary

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

The NM_152791.5(ZNF555):​c.*3337A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,182 control chromosomes in the GnomAD database, including 55,187 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 0.85 (55187 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ZNF555 NM_152791.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 8 publications found

Genes affected

ZNF555 (HGNC:28382): (zinc finger protein 555) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267063 (HGNC:58567):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF555	NM_152791.5	c.*3337A>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000334241.9	NP_690004.4
ZNF555	NM_001172775.2	c.*3337A>C		3_prime_UTR_variant	Exon 4 of 4		NP_001166246.1
ZNF555	XM_011527716.3	c.*3337A>C		3_prime_UTR_variant	Exon 4 of 4		XP_011526018.1
ZNF555	XM_017026375.2	c.*3337A>C		3_prime_UTR_variant	Exon 4 of 4		XP_016881864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF555	ENST00000334241.9	c.*3337A>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_152791.5	ENSP00000334853.3
ENSG00000267063	ENST00000589365.1	n.397+1031T>G		intron_variant	Intron 1 of 1	4
ENSG00000267063	ENST00000728256.1	n.350+1031T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129266 AN: 152062 Hom.: 55136 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.855

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.850 AC: 129372 AN: 152182 Hom.: 55187 Cov.: 33 AF XY: 0.854 AC XY: 63559 AN XY: 74430

African (AFR) AF: 0.805 AC: 33400 AN: 41476

American (AMR) AF: 0.887 AC: 13553 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2893 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5182 AN: 5184

South Asian (SAS) AF: 0.964 AC: 4652 AN: 4826

European-Finnish (FIN) AF: 0.869 AC: 9219 AN: 10604

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57590 AN: 68012

Other (OTH) AF: 0.856 AC: 1811 AN: 2116

Alfa AF: 0.849 Hom.: 144936

Bravo AF: 0.848

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.37
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4807347; hg19: chr19-2857287;