chr19-52585180-A-C

Position:

• chr19-52585180-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018260.3(ZNF701):​c.*1723A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,238 control chromosomes in the GnomAD database, including 37,484 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 0.70 (37441 hom., cov: 32)
  • Exomes 𝑓: 0.76 (43 hom.)
• Consequence: ZNF701 NM_018260.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26

Genes affected

ZNF701 (HGNC:25597): (zinc finger protein 701) 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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF701	NM_018260.3	c.*1723A>C		3_prime_UTR_variant	4/4	ENST00000391785.8	NP_060730.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF701	ENST00000391785.8	c.*1723A>C		3_prime_UTR_variant	4/4	1	NM_018260.3	ENSP00000375662	P2
ZNF701	ENST00000540331.1	c.*1723A>C		3_prime_UTR_variant	5/5	1		ENSP00000444339	A2
	ENST00000599222.1	n.382T>G		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106194 AN: 151976 Hom.: 37390 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.703

GnomAD4 exome AF: 0.757 AC: 109 AN: 144 Hom.: 43 Cov.: 0 AF XY: 0.804 AC XY: 90 AN XY: 112

Gnomad4 AFR exome AF: 0.600

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.746

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.699 AC: 106309 AN: 152094 Hom.: 37441 Cov.: 32 AF XY: 0.695 AC XY: 51715 AN XY: 74364

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.708

Alfa AF: 0.688 Hom.: 4580

Bravo AF: 0.694

Asia WGS AF: 0.636 AC: 2214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs179320; hg19: chr19-53088433;