rs4801931

Variant names:

• chr19-52732993-C-T
• rs4801931
• NM_001161499.2:c.-222+2008G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001161499.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF611	NM_001161499.2	MANE Select	c.-222+2008G>A		intron	N/A	NP_001154971.1	Q8N823-1
	ZNF611	NM_001161500.2		c.-122+2008G>A		intron	N/A	NP_001154972.1	Q8N823-1
	ZNF611	NM_001161501.1		c.-302+2008G>A		intron	N/A	NP_001154973.1	Q8N823-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF611	ENST00000652185.1	MANE Select	c.-222+2008G>A		intron	N/A	ENSP00000498713.1	Q8N823-1
	ZNF611	ENST00000595001.5	TSL:1	n.-345+2008G>A		intron	N/A	ENSP00000471243.1	M0QYZ5
	ZNF611	ENST00000540744.5	TSL:4	c.-122+2008G>A		intron	N/A	ENSP00000439211.1	Q8N823-1

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

African (AFR) AF: 0.720 AC: 29700 AN: 41276

American (AMR) AF: 0.577 AC: 8773 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2112 AN: 3464

East Asian (EAS) AF: 0.525 AC: 2701 AN: 5140

South Asian (SAS) AF: 0.552 AC: 2656 AN: 4808

European-Finnish (FIN) AF: 0.566 AC: 5938 AN: 10482

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43332 AN: 67892

Other (OTH) AF: 0.617 AC: 1298 AN: 2104

Alfa AF: 0.636 Hom.: 114550

Bravo AF: 0.647

Asia WGS AF: 0.541 AC: 1878 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.17
PhyloP100		-0.76
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: rs4801931; hg19: chr19-53236246;