3-179338347-A-T

Variant names:

• chr3-179338347-A-T
• rs10460887
• NM_001303426.2:c.*3925A>T

Variant summary

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

The NM_001303426.2(ZNF639):​c.*3925A>T 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: 32)
• Consequence: ZNF639 NM_001303426.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 7 publications found

Genes affected

ZNF639 (HGNC:30950): (zinc finger protein 639) This gene encodes a member of the Kruppel-like zinc finger family of proteins. Amplification and overexpression of this gene have been observed in esophageal squamous cell carcinoma. The encoded protein has been shown to bind DNA in a sequence-specific manner and may regulate HIV-1 gene expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

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=-0.53).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303426.2. 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
	ZNF639	NM_001303426.2	MANE Select	c.*3925A>T		3_prime_UTR	Exon 6 of 6	NP_001290355.1	Q9UID6
	ZNF639	NM_001303425.2		c.*3925A>T		3_prime_UTR	Exon 7 of 7	NP_001290354.1	Q9UID6
	ZNF639	NM_001375800.1		c.*3925A>T		3_prime_UTR	Exon 7 of 7	NP_001362729.1	Q9UID6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF639	ENST00000496856.6	TSL:1 MANE Select	c.*3925A>T		3_prime_UTR	Exon 6 of 6	ENSP00000417740.1	Q9UID6
	ZNF639	ENST00000326361.7	TSL:1	c.*3925A>T		3_prime_UTR	Exon 7 of 7	ENSP00000325634.3	Q9UID6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	9.1
DANN	Benign	0.91
PhyloP100		0.96

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10460887; hg19: chr3-179056135;