19-53067614-C-T

Variant names:

• chr19-53067614-C-T
• rs10405102
• NM_001322131.2:c.*463G>A

Variant summary

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

The NM_001322131.2(ZNF160):​c.*463G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 154,218 control chromosomes in the GnomAD database, including 15,393 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 0.43 (15250 hom., cov: 32)
  • Exomes 𝑓: 0.33 (143 hom.)
• Consequence: ZNF160 NM_001322131.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 10 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]

ENSG00000306331 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF160	NM_001322131.2	c.*463G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000683776.1	NP_001309060.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF160	ENST00000683776.1	c.*463G>A		3_prime_UTR_variant	Exon 6 of 6		NM_001322131.2	ENSP00000507845.1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64877 AN: 151880 Hom.: 15205 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.425

GnomAD4 exome AF: 0.332 AC: 737 AN: 2220 Hom.: 143 Cov.: 0 AF XY: 0.319 AC XY: 338 AN XY: 1060

African (AFR) AF: 0.600 AC: 24 AN: 40

American (AMR) AF: 0.365 AC: 105 AN: 288

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 18 AN: 46

East Asian (EAS) AF: 0.0714 AC: 2 AN: 28

South Asian (SAS) AF: 0.337 AC: 33 AN: 98

European-Finnish (FIN) AF: 0.260 AC: 13 AN: 50

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.322 AC: 512 AN: 1588

Other (OTH) AF: 0.366 AC: 30 AN: 82

GnomAD4 genome AF: 0.427 AC: 64977 AN: 151998 Hom.: 15250 Cov.: 32 AF XY: 0.420 AC XY: 31232 AN XY: 74306

African (AFR) AF: 0.625 AC: 25902 AN: 41456

American (AMR) AF: 0.399 AC: 6086 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1446 AN: 3468

East Asian (EAS) AF: 0.109 AC: 560 AN: 5158

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4814

European-Finnish (FIN) AF: 0.321 AC: 3392 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24794 AN: 67974

Other (OTH) AF: 0.426 AC: 899 AN: 2108

Alfa AF: 0.385 Hom.: 35832

Bravo AF: 0.440

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		-1.2
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: rs10405102; hg19: chr19-53570867;