rs1402752

chr3-44645808-G-Achr3-44645808-G-C

Variant summary

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

The NM_006991.5(ZNF197):c.*1588G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 985,302 control chromosomes in the GnomAD database, including 349,112 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 0.85 (55331 hom., cov: 32)
  • Exomes 𝑓: 0.84 (293781 hom.)
• Consequence: ZNF197 NM_006991.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

ZNF197 (HGNC:12988): (zinc finger protein 197) This gene product belongs to the zinc finger protein superfamily, members of which are regulatory proteins characterized by nucleic acid-binding zinc finger domains. The encoded protein contains 20 tandemly arrayed C2H2-type zinc fingers, a Kruppel-associated box (KRAB) domain, and a SCAN box. This transcript turns over rapidly and contains 3' UTR AUUUA motifs, which are often a hallmark of rapid turnover. It is overexpressed in some thyroid papillary carcinomas. This gene is located in a cluster of zinc finger genes at 3p21. Naturally-occurring readthrough transcription is observed between this gene and the upstream zinc finger protein 660 gene and is represented by GeneID:110354863. [provided by RefSeq, May 2017]

ZNF660-ZNF197 (HGNC:):

ZKSCAN7-AS1 (HGNC:53964): (ZKSCAN7 ZNF cluster antisense RNA 1)

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 (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF197	NM_006991.5	c.*1588G>A		3_prime_UTR_variant	6/6	ENST00000344387.9
ZNF660-ZNF197	NR_147692.2	n.5045G>A		non_coding_transcript_exon_variant	8/8
ZKSCAN7-AS1	NR_157564.1	n.220+15454C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF197	ENST00000344387.9	c.*1588G>A		3_prime_UTR_variant	6/6	1	NM_006991.5	P1
ZKSCAN7-AS1	ENST00000457331.2	n.232+15454C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129612 AN: 152090 Hom.: 55284 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.863

GnomAD4 exome AF: 0.840 AC: 699557 AN: 833094 Hom.: 293781 Cov.: 52 AF XY: 0.840 AC XY: 323028 AN XY: 384710

Gnomad4 AFR exome AF: 0.853

Gnomad4 AMR exome AF: 0.783

Gnomad4 ASJ exome AF: 0.905

Gnomad4 EAS exome AF: 0.875

Gnomad4 SAS exome AF: 0.825

Gnomad4 FIN exome AF: 0.877

Gnomad4 NFE exome AF: 0.839

Gnomad4 OTH exome AF: 0.850

GnomAD4 genome AF: 0.852 AC: 129710 AN: 152208 Hom.: 55331 Cov.: 32 AF XY: 0.855 AC XY: 63594 AN XY: 74420

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.857

Alfa AF: 0.853 Hom.: 71289

Bravo AF: 0.848

Asia WGS AF: 0.839 AC: 2920 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	0.35
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402752; hg19: chr3-44687300;