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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF639	NM_001303426.2	c.*3925A>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000496856.6	NP_001290355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF639	ENST00000496856.6	c.*3925A>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_001303426.2	ENSP00000417740.1
ZNF639	ENST00000326361.7	c.*3925A>G		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000325634.3

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

Gnomad4 AFR exome AC: 0 AN: 0

Gnomad4 AMR exome AC: 0 AN: 0

Gnomad4 ASJ exome AC: 0 AN: 0

Gnomad4 EAS exome AC: 0 AN: 0

Gnomad4 SAS exome AC: 0 AN: 0

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 6

Gnomad4 NFE exome AC: 0 AN: 0

Gnomad4 Remaining exome 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

Gnomad4 AFR AF: 0.131 AC: 0.131012 AN: 0.131012

Gnomad4 AMR AF: 0.235 AC: 0.234786 AN: 0.234786

Gnomad4 ASJ AF: 0.194 AC: 0.193595 AN: 0.193595

Gnomad4 EAS AF: 0.217 AC: 0.216853 AN: 0.216853

Gnomad4 SAS AF: 0.194 AC: 0.194203 AN: 0.194203

Gnomad4 FIN AF: 0.151 AC: 0.150945 AN: 0.150945

Gnomad4 NFE AF: 0.177 AC: 0.177275 AN: 0.177275

Gnomad4 OTH AF: 0.191 AC: 0.190521 AN: 0.190521

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.8
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10460887; hg19: chr3-179056135;