NM_001322131.2:c.-354+1471T>C

Variant names:

• chr19-53101794-A-G
• rs17300167
• NM_001322131.2:c.-354+1471T>C

Variant summary

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

The NM_001322131.2(ZNF160):​c.-354+1471T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.05 in 152,324 control chromosomes in the GnomAD database, including 285 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 0.050 (285 hom., cov: 34)
• Consequence: ZNF160 NM_001322131.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF160	NM_001322131.2	c.-354+1471T>C		intron_variant	Intron 1 of 5	ENST00000683776.1	NP_001309060.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF160	ENST00000683776.1	c.-354+1471T>C		intron_variant	Intron 1 of 5		NM_001322131.2	ENSP00000507845.1

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7608 AN: 152206 Hom.: 285 Cov.: 34

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0500 AC: 7612 AN: 152324 Hom.: 285 Cov.: 34 AF XY: 0.0483 AC XY: 3597 AN XY: 74486

African (AFR) AF: 0.0146 AC: 609 AN: 41582

American (AMR) AF: 0.0458 AC: 700 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4828

European-Finnish (FIN) AF: 0.0590 AC: 626 AN: 10618

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0768 AC: 5226 AN: 68026

Other (OTH) AF: 0.0417 AC: 88 AN: 2112

Alfa AF: 0.0642 Hom.: 285

Bravo AF: 0.0490

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.66
PhyloP100		0.37
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: rs17300167; hg19: chr19-53605047;