NM_198535.3:c.*4447C>T

Variant names:

• chr19-9291028-G-A
• rs7247108
• NM_198535.3:c.*4447C>T

Variant summary

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

The NM_198535.3(ZNF699):​c.*4447C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,792 control chromosomes in the GnomAD database, including 29,052 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 0.61 (29052 hom., cov: 32)
• Consequence: ZNF699 NM_198535.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

ZNF699 (HGNC:24750): (zinc finger protein 699) 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF699	NM_198535.3	c.*4447C>T		downstream_gene_variant		ENST00000591998.6	NP_940937.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF699	ENST00000591998.6	c.*4447C>T		downstream_gene_variant		5	NM_198535.3	ENSP00000467723.1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93023 AN: 151674 Hom.: 29012 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.613 AC: 93117 AN: 151792 Hom.: 29052 Cov.: 32 AF XY: 0.607 AC XY: 44994 AN XY: 74174

African (AFR) AF: 0.723 AC: 29982 AN: 41442

American (AMR) AF: 0.582 AC: 8874 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2441 AN: 5168

South Asian (SAS) AF: 0.589 AC: 2840 AN: 4818

European-Finnish (FIN) AF: 0.454 AC: 4754 AN: 10460

Middle Eastern (MID) AF: 0.646 AC: 186 AN: 288

European-Non Finnish (NFE) AF: 0.589 AC: 39972 AN: 67878

Other (OTH) AF: 0.630 AC: 1325 AN: 2104

Alfa AF: 0.602 Hom.: 15460

Bravo AF: 0.629

Asia WGS AF: 0.546 AC: 1882 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.60
PhyloP100		-0.36

Splicing

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

Publications

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Other links and lift over

dbSNP: rs7247108; hg19: chr19-9401704;