16-3403882-A-G

Variant names:

• chr16-3403882-A-G
• rs37812
• NM_003450.3:c.403-544A>G

Variant summary

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

The NM_003450.3(ZNF174):​c.403-544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,216 control chromosomes in the GnomAD database, including 61,093 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 0.90 (61093 hom., cov: 32)
• Consequence: ZNF174 NM_003450.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 1 publications found

Genes affected

ZNF174 (HGNC:12963): (zinc finger protein 174) This gene encodes a protein with three Cys2-His2-type zinc fingers in the carboxy-terminus, a putative nuclear localization signal, and an amino-terminus SCAN box which forms homodimers. This protein is believed to function as a transcriptional repressor. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Dec 2016]

ENSG00000285329 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003450.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF174	NM_003450.3	MANE Select	c.403-544A>G		intron	N/A	NP_003441.1
	ZNF174	NM_001347868.2		c.403-544A>G		intron	N/A	NP_001334797.1
	ZNF174	NM_001347869.2		c.403-544A>G		intron	N/A	NP_001334798.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF174	ENST00000268655.5	TSL:1 MANE Select	c.403-544A>G		intron	N/A	ENSP00000268655.4
	ZNF174	ENST00000572544.1	TSL:1	c.403-544A>G		intron	N/A	ENSP00000459681.1
	ZNF174	ENST00000344823.9	TSL:1	c.403-544A>G		intron	N/A	ENSP00000339781.5

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136137 AN: 152098 Hom.: 61040 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.895 AC: 136249 AN: 152216 Hom.: 61093 Cov.: 32 AF XY: 0.895 AC XY: 66565 AN XY: 74404

African (AFR) AF: 0.952 AC: 39564 AN: 41538

American (AMR) AF: 0.904 AC: 13827 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2805 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4666 AN: 5180

South Asian (SAS) AF: 0.894 AC: 4306 AN: 4816

European-Finnish (FIN) AF: 0.852 AC: 9024 AN: 10588

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59209 AN: 68008

Other (OTH) AF: 0.866 AC: 1833 AN: 2116

Alfa AF: 0.886 Hom.: 7722

Bravo AF: 0.903

Asia WGS AF: 0.916 AC: 3185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.54
PhyloP100		-0.20
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: rs37812; hg19: chr16-3453882;