5-179080269-A-C

Variant names:

• chr5-179080269-A-C
• rs1445844
• NM_014594.3:c.*172A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014594.3(ZNF354C):​c.*172A>C variant causes a 3 prime UTR 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF354C NM_014594.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 11 publications found

Genes affected

ZNF354C (HGNC:16736): (zinc finger protein 354C) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF354C	NM_014594.3	c.*172A>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000315475.7	NP_055409.1
ZNF354C	XM_017009409.2	c.*172A>C		3_prime_UTR_variant	Exon 5 of 5		XP_016864898.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF354C	ENST00000315475.7	c.*172A>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_014594.3	ENSP00000324064.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 279612 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 142762

African (AFR) AF: 0.00 AC: 0 AN: 7432

American (AMR) AF: 0.00 AC: 0 AN: 10066

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9114

East Asian (EAS) AF: 0.00 AC: 0 AN: 22444

South Asian (SAS) AF: 0.00 AC: 0 AN: 9220

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23372

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1246

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 179458

Other (OTH) AF: 0.00 AC: 0 AN: 17260

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.7
DANN	Benign	0.84
PhyloP100		0.33

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: rs1445844; hg19: chr5-178507270;