rs11084211

Positions:

• chr19-52957608-G-A

Variant summary

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

The NM_001202457.3(ZNF816):​c.-15-1504C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,958 control chromosomes in the GnomAD database, including 15,040 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 0.43 (15040 hom., cov: 31)
• Consequence: ZNF816 NM_001202457.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ZNF816 (HGNC:26995): (zinc finger protein 816) 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 integral component of membrane. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF816-ZNF321P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF816	NM_001202457.3	c.-15-1504C>T		intron_variant		ENST00000444460.7	NP_001189386.1
ZNF816-ZNF321P	NM_001202473.2	c.-15-1504C>T		intron_variant			NP_001189402.1
ZNF816	NM_001031665.4	c.-15-1504C>T		intron_variant			NP_001026835.1
ZNF816	NM_001202456.3	c.-15-1504C>T		intron_variant			NP_001189385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF816	ENST00000444460.7	c.-15-1504C>T		intron_variant		1	NM_001202457.3	ENSP00000403266	P1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64710 AN: 151840 Hom.: 15016 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.426 AC: 64777 AN: 151958 Hom.: 15040 Cov.: 31 AF XY: 0.425 AC XY: 31543 AN XY: 74260

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.437

Alfa AF: 0.375 Hom.: 5635

Bravo AF: 0.436

Asia WGS AF: 0.411 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.71

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: rs11084211; hg19: chr19-53460861;