rs10460887

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-179338347-A-G
• chr3-179338347-A-T

Variant summary

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

The NM_001303426.2(ZNF639):​c.*3925A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,144 control chromosomes in the GnomAD database, including 2,336 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 0.17 (2336 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

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>G		3_prime_UTR	Exon 6 of 6	NP_001290355.1	Q9UID6
	ZNF639	NM_001303425.2		c.*3925A>G		3_prime_UTR	Exon 7 of 7	NP_001290354.1	Q9UID6
	ZNF639	NM_001375800.1		c.*3925A>G		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>G		3_prime_UTR	Exon 6 of 6	ENSP00000417740.1	Q9UID6
	ZNF639	ENST00000326361.7	TSL:1	c.*3925A>G		3_prime_UTR	Exon 7 of 7	ENSP00000325634.3	Q9UID6

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26036 AN: 152026 Hom.: 2335 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.192

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.171 AC: 26043 AN: 152144 Hom.: 2336 Cov.: 32 AF XY: 0.174 AC XY: 12966 AN XY: 74400

African (AFR) AF: 0.131 AC: 5437 AN: 41500

American (AMR) AF: 0.235 AC: 3588 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 671 AN: 3466

East Asian (EAS) AF: 0.217 AC: 1122 AN: 5174

South Asian (SAS) AF: 0.194 AC: 938 AN: 4830

European-Finnish (FIN) AF: 0.151 AC: 1597 AN: 10580

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12054 AN: 67996

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.182 Hom.: 4216

Bravo AF: 0.179

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.8
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;