rs2074066

Positions:

• chr19-57477028-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144068.2(ZNF772):​c.33+249G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,100 control chromosomes in the GnomAD database, including 7,789 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 0.31 (7789 hom., cov: 32)
• Consequence: ZNF772 NM_001144068.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

Genes affected

ZNF772 (HGNC:33106): (zinc finger protein 772) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF772	NM_001144068.2	c.33+249G>A		intron_variant		ENST00000356584.8
ZNF772	NM_001024596.3	c.33+249G>A		intron_variant
ZNF772	NM_001330613.2	c.-54+249G>A		intron_variant
ZNF772	XM_005258944.5	c.-15+249G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF772	ENST00000356584.8	c.33+249G>A		intron_variant		2	NM_001144068.2	A2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47686 AN: 151980 Hom.: 7779 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0996

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.314 AC: 47712 AN: 152100 Hom.: 7789 Cov.: 32 AF XY: 0.308 AC XY: 22891 AN XY: 74354

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.0990

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.324

Alfa AF: 0.317 Hom.: 1037

Bravo AF: 0.313

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.9
DANN	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs2074066; hg19: chr19-57988396;