rs4801931

Positions:

• chr19-52732993-C-T

Variant summary

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

The NM_001161499.2(ZNF611):​c.-222+2008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 151,574 control chromosomes in the GnomAD database, including 31,544 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 0.64 (31544 hom., cov: 28)
• Consequence: ZNF611 NM_001161499.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

Genes affected

ZNF611 (HGNC:28766): (zinc finger protein 611) 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF611	NM_001161499.2	c.-222+2008G>A		intron_variant		ENST00000652185.1	NP_001154971.1
ZNF611	NM_001161500.2	c.-122+2008G>A		intron_variant			NP_001154972.1
ZNF611	NM_001161501.1	c.-302+2008G>A		intron_variant			NP_001154973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF611	ENST00000652185.1	c.-222+2008G>A		intron_variant			NM_001161499.2	ENSP00000498713	P1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97293 AN: 151452 Hom.: 31504 Cov.: 28

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.642 AC: 97381 AN: 151574 Hom.: 31544 Cov.: 28 AF XY: 0.638 AC XY: 47250 AN XY: 74076

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.617

Alfa AF: 0.632 Hom.: 56477

Bravo AF: 0.647

Asia WGS AF: 0.541 AC: 1878 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.17

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: rs4801931; hg19: chr19-53236246;