chr19-2857289-A-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_152791.5(ZNF555):​c.*3337A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF555	NM_152791.5	c.*3337A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000334241.9	NP_690004.4
ZNF555	NM_001172775.2	c.*3337A>G		3_prime_UTR_variant	Exon 4 of 4		NP_001166246.1
ZNF555	XM_011527716.3	c.*3337A>G		3_prime_UTR_variant	Exon 4 of 4		XP_011526018.1
ZNF555	XM_017026375.2	c.*3337A>G		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>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_152791.5	ENSP00000334853.3
ENSG00000267063	ENST00000589365.1	n.397+1031T>C		intron_variant	Intron 1 of 1	4
ENSG00000267063	ENST00000728256.1	n.350+1031T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		-0.83

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;