19-52948038-T-C

Variant names:

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

Variant summary

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

The NM_001202473.2(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 NM_001202473.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF816-ZNF321P	NM_001202473.2	c.190+4713A>G		intron_variant	Intron 3 of 3		NP_001189402.1
LOC124904761	XR_007067329.1	n.671T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF816-ZNF321P	ENST00000391777.3	c.190+4713A>G		intron_variant	Intron 3 of 3	2		ENSP00000375656.3

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

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.428

Alfa AF: 0.360 Hom.: 10788

Bravo AF: 0.420

Asia WGS AF: 0.395 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.29

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: rs9304742; hg19: chr19-53451291;