chr19-2857289-A-C

Position:

• chr19-2857289-A-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF555	NM_152791.5	c.*3337A>C		3_prime_UTR_variant	4/4	ENST00000334241.9	NP_690004.4
ZNF555	NM_001172775.2	c.*3337A>C		3_prime_UTR_variant	4/4		NP_001166246.1
ZNF555	XM_011527716.3	c.*3337A>C		3_prime_UTR_variant	4/4		XP_011526018.1
ZNF555	XM_017026375.2	c.*3337A>C		3_prime_UTR_variant	4/4		XP_016881864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF555	ENST00000334241.9	c.*3337A>C		3_prime_UTR_variant	4/4	1	NM_152791.5	ENSP00000334853	P4
	ENST00000589365.1	n.397+1031T>G		intron_variant, non_coding_transcript_variant		4

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

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

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.856

Alfa AF: 0.852 Hom.: 93985

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4807347; hg19: chr19-2857287;