rs4804628

Variant names:

• chr19-11659622-G-C
• rs4804628
• ENST00000747612.1:n.1059G>C

Variant summary

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

The ENST00000747612.1(ZNF833P):​n.1059G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,086 control chromosomes in the GnomAD database, including 34,644 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 0.67 (34644 hom., cov: 33)
• Consequence: ZNF833P ENST00000747612.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 4 publications found

Genes affected

ZNF833P (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747612.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF833P	ENST00000747612.1		n.1059G>C		non_coding_transcript_exon	Exon 5 of 5
	ZNF833P	ENST00000344893.4	TSL:2	n.880+7569G>C		intron	N/A
	ZNF833P	ENST00000666937.1		n.732+7569G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101417 AN: 151968 Hom.: 34607 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.667 AC: 101505 AN: 152086 Hom.: 34644 Cov.: 33 AF XY: 0.665 AC XY: 49414 AN XY: 74326

African (AFR) AF: 0.809 AC: 33610 AN: 41524

American (AMR) AF: 0.644 AC: 9826 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2574 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3803 AN: 5176

South Asian (SAS) AF: 0.617 AC: 2975 AN: 4824

European-Finnish (FIN) AF: 0.566 AC: 5977 AN: 10562

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40620 AN: 67960

Other (OTH) AF: 0.689 AC: 1456 AN: 2112

Alfa AF: 0.632 Hom.: 3867

Bravo AF: 0.681

Asia WGS AF: 0.710 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.43
PhyloP100		-0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4804628; hg19: chr19-11770437;