19-53077898-T-C

Position:

• chr19-53077898-T-C

Variant summary

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

The NM_001322131.2(ZNF160):​c.16-2715A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,514 control chromosomes in the GnomAD database, including 10,785 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 0.37 (10785 hom., cov: 31)
• Consequence: ZNF160 NM_001322131.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

ZNF160 (HGNC:12948): (zinc finger protein 160) The protein encoded by this gene is a Kruppel-related zinc finger protein which is characterized by the presence of an N-terminal repressor domain, the Kruppel-associated box (KRAB). The KRAB domain is a potent repressor of transcription; thus this protein may function in transcription regulation. Multiple transcript variants have been found for this gene. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF160	NM_001322131.2	c.16-2715A>G		intron_variant		ENST00000683776.1	NP_001309060.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF160	ENST00000683776.1	c.16-2715A>G		intron_variant			NM_001322131.2	ENSP00000507845	P1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55731 AN: 151396 Hom.: 10776 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.368 AC: 55778 AN: 151514 Hom.: 10785 Cov.: 31 AF XY: 0.363 AC XY: 26869 AN XY: 73992

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.367

Alfa AF: 0.341 Hom.: 11642

Bravo AF: 0.378

Asia WGS AF: 0.328 AC: 1141 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	4.4
DANN	Benign	0.48

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: rs7254015; hg19: chr19-53581151;