rs11878803

Variant names:

• chr19-51998068-G-A
• rs11878803
• NM_001199324.2:c.271+2278C>T

Variant summary

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

The NM_001199324.2(ZNF615):​c.271+2278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,072 control chromosomes in the GnomAD database, including 1,057 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 0.11 (1057 hom., cov: 32)
• Consequence: ZNF615 NM_001199324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 2 publications found

Genes affected

ZNF615 (HGNC:24740): (zinc finger protein 615) Predicted to enable DNA-binding transcription activator 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199324.2. 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
	ZNF615	NM_001199324.2	MANE Select	c.271+2278C>T		intron	N/A	NP_001186253.1	Q8N8J6-2
	ZNF615	NM_001321323.2		c.286+2278C>T		intron	N/A	NP_001308252.1
	ZNF615	NM_001321319.2		c.271+2278C>T		intron	N/A	NP_001308248.1	Q8N8J6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF615	ENST00000598071.6	TSL:1 MANE Select	c.271+2278C>T		intron	N/A	ENSP00000471041.1	Q8N8J6-2
	ZNF615	ENST00000594083.5	TSL:1	c.271+2278C>T		intron	N/A	ENSP00000471549.1	Q8N8J6-2
	ZNF615	ENST00000618487.4	TSL:1	c.271+2278C>T		intron	N/A	ENSP00000483676.1	Q8N8J6-2

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16474 AN: 151954 Hom.: 1055 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.109 AC: 16508 AN: 152072 Hom.: 1057 Cov.: 32 AF XY: 0.113 AC XY: 8382 AN XY: 74346

African (AFR) AF: 0.150 AC: 6207 AN: 41452

American (AMR) AF: 0.158 AC: 2419 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3472

East Asian (EAS) AF: 0.125 AC: 646 AN: 5188

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4824

European-Finnish (FIN) AF: 0.0587 AC: 620 AN: 10564

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4780 AN: 67974

Other (OTH) AF: 0.113 AC: 239 AN: 2114

Alfa AF: 0.0880 Hom.: 382

Bravo AF: 0.116

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.7
DANN	Benign	0.80
PhyloP100		0.16
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: rs11878803; hg19: chr19-52501321;