rs761098156

Variant names:

• chr16-3408899-C-A
• rs761098156
• NM_003450.3:c.1204C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-3408899-C-A
• chr16-3408899-C-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_003450.3(ZNF174):​c.1204C>A​(p.Arg402Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ZNF174 NM_003450.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 0 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP7: Synonymous conserved (PhyloP=0.028 with no splicing effect.

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.1204C>A	p.Arg402Arg	synonymous	Exon 3 of 3	NP_003441.1	Q15697-1
	ZNF174	NM_001347868.2		c.1204C>A	p.Arg402Arg	synonymous	Exon 4 of 4	NP_001334797.1	Q15697-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF174	ENST00000268655.5	TSL:1 MANE Select	c.1204C>A	p.Arg402Arg	synonymous	Exon 3 of 3	ENSP00000268655.4	Q15697-1
	ENSG00000285329	ENST00000575785.2	TSL:4	n.211+4251C>A		intron	N/A	ENSP00000477472.1	V9GZ69
	ZNF174	ENST00000571936.5	TSL:5	c.1204C>A	p.Arg402Arg	synonymous	Exon 4 of 4	ENSP00000460397.1	Q15697-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.4
DANN	Benign	0.45
PhyloP100		0.028

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: rs761098156; hg19: chr16-3458899;