chr19-52948038-T-C

Variant names:

• chr19-52948038-T-C
• rs9304742
• ENST00000391777.3:c.190+4713A>G

Variant summary

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

The ENST00000391777.3(ZNF816-ZNF321P):​c.190+4713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,754 control chromosomes in the GnomAD database, including 13,982 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 0.41 (13982 hom., cov: 31)
• Consequence: ZNF816-ZNF321P ENST00000391777.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 32 publications found

Genes affected

ZNF816-ZNF321P (HGNC:38879): (ZNF816-ZNF321P readthrough) This locus represents naturally occurring read-through transcription between the zinc finger protein 816 (ZNF816) gene and the zinc finger protein 321 (ZNF321) pseudogene on chromosome 19. The read-through transcript encodes a KRAB domain-containing protein that shares sequence identity with the upstream gene product, but it contains a distinct C-terminus encoded by exon structure from the downstream pseudogene. [provided by RefSeq, Jan 2011]

LOC124904761 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000391777.3. 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
	ZNF816-ZNF321P	NM_001202473.2		c.190+4713A>G		intron	N/A	NP_001189402.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF816-ZNF321P	ENST00000391777.3	TSL:2	c.190+4713A>G		intron	N/A	ENSP00000375656.3
	ENSG00000306382	ENST00000817332.1		n.346+1234T>C		intron	N/A
	ENSG00000306382	ENST00000817333.1		n.124+1234T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62540 AN: 151638 Hom.: 13953 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.413 AC: 62630 AN: 151754 Hom.: 13982 Cov.: 31 AF XY: 0.411 AC XY: 30430 AN XY: 74118

African (AFR) AF: 0.587 AC: 24254 AN: 41328

American (AMR) AF: 0.327 AC: 4985 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1700 AN: 5162

South Asian (SAS) AF: 0.435 AC: 2096 AN: 4814

European-Finnish (FIN) AF: 0.302 AC: 3165 AN: 10486

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23476 AN: 67938

Other (OTH) AF: 0.428 AC: 901 AN: 2104

Alfa AF: 0.373 Hom.: 18298

Bravo AF: 0.420

Asia WGS AF: 0.395 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.29
PhyloP100		-1.0
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: rs9304742; hg19: chr19-53451291;