19-53098161-C-G

Variant names:

• chr19-53098161-C-G
• rs10406237
• NM_001322131.2:c.-354+5104G>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+5104G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,196 control chromosomes in the GnomAD database, including 2,252 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 0.16 (2252 hom., cov: 32)
• Consequence: ZNF160 NM_001322131.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 2 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322131.2. 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
	ZNF160	NM_001322131.2	MANE Select	c.-354+5104G>C		intron	N/A	NP_001309060.1
	ZNF160	NM_001102603.2		c.-247+5104G>C		intron	N/A	NP_001096073.1
	ZNF160	NM_001322128.2		c.-255+5104G>C		intron	N/A	NP_001309057.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF160	ENST00000683776.1	MANE Select	c.-354+5104G>C		intron	N/A	ENSP00000507845.1
	ZNF160	ENST00000418871.5	TSL:1	c.-130+5104G>C		intron	N/A	ENSP00000409597.1
	ZNF160	ENST00000599056.5	TSL:1	c.-215+5104G>C		intron	N/A	ENSP00000470961.1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24332 AN: 152078 Hom.: 2249 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.160 AC: 24348 AN: 152196 Hom.: 2252 Cov.: 32 AF XY: 0.156 AC XY: 11570 AN XY: 74400

African (AFR) AF: 0.235 AC: 9732 AN: 41498

American (AMR) AF: 0.129 AC: 1979 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.0707 AC: 341 AN: 4826

European-Finnish (FIN) AF: 0.0793 AC: 841 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10170 AN: 68004

Other (OTH) AF: 0.167 AC: 351 AN: 2108

Alfa AF: 0.0750 Hom.: 102

Bravo AF: 0.170

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.87
PhyloP100		0.36
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: rs10406237; hg19: chr19-53601414;