rs1610062

Variant names:

• chr19-2843535-G-A
• rs1610062
• NM_152791.5:c.3+1960G>A

Variant summary

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

The NM_152791.5(ZNF555):​c.3+1960G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,072 control chromosomes in the GnomAD database, including 36,626 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 0.69 (36626 hom., cov: 32)
• Consequence: ZNF555 NM_152791.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 3 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]

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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF555	NM_152791.5	c.3+1960G>A		intron_variant	Intron 1 of 3	ENST00000334241.9	NP_690004.4
ZNF555	NM_001172775.2	c.3+1960G>A		intron_variant	Intron 1 of 3		NP_001166246.1
ZNF555	XM_011527716.3	c.9+1248G>A		intron_variant	Intron 1 of 3		XP_011526018.1
ZNF555	XM_017026375.2	c.9+1248G>A		intron_variant	Intron 1 of 3		XP_016881864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF555	ENST00000334241.9	c.3+1960G>A		intron_variant	Intron 1 of 3	1	NM_152791.5	ENSP00000334853.3
ZNF555	ENST00000591539.1	c.3+1960G>A		intron_variant	Intron 1 of 3	2		ENSP00000467893.1
ZNF555	ENST00000585966.5	c.-94+2052G>A		intron_variant	Intron 1 of 3	4		ENSP00000466982.1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105132 AN: 151954 Hom.: 36590 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.692 AC: 105220 AN: 152072 Hom.: 36626 Cov.: 32 AF XY: 0.697 AC XY: 51808 AN XY: 74346

African (AFR) AF: 0.662 AC: 27451 AN: 41470

American (AMR) AF: 0.761 AC: 11621 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2375 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4118 AN: 5170

South Asian (SAS) AF: 0.777 AC: 3745 AN: 4822

European-Finnish (FIN) AF: 0.757 AC: 8017 AN: 10584

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45577 AN: 67964

Other (OTH) AF: 0.705 AC: 1490 AN: 2112

Alfa AF: 0.680 Hom.: 135292

Bravo AF: 0.687

Asia WGS AF: 0.777 AC: 2699 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	1.6
DANN	Benign	0.51
PhyloP100		-0.099
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: rs1610062; hg19: chr19-2843533;