rs1402752

Variant names:

• chr3-44645808-G-A
• rs1402752
• NM_006991.5:c.*1588G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-44645808-G-A
• chr3-44645808-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006991.5. 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
	ZNF197	NM_006991.5	MANE Select	c.*1588G>A		3_prime_UTR	Exon 6 of 6	NP_008922.1	O14709-1
	ZNF197	NM_001323293.2		c.*1588G>A		3_prime_UTR	Exon 6 of 6	NP_001310222.1	O14709-1
	ZNF660-ZNF197	NM_001351732.2		c.*1588G>A		3_prime_UTR	Exon 7 of 7	NP_001338661.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF197	ENST00000344387.9	TSL:1 MANE Select	c.*1588G>A		3_prime_UTR	Exon 6 of 6	ENSP00000345809.4	O14709-1
	ZNF197	ENST00000383744.8	TSL:1	c.770-683G>A		intron	N/A	ENSP00000373250.4	O14709-2
	ZNF197	ENST00000383745.6	TSL:1	c.770-683G>A		intron	N/A	ENSP00000373251.2	O14709-2

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

African (AFR) AF: 0.853 AC: 13461 AN: 15786

American (AMR) AF: 0.783 AC: 770 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 4661 AN: 5152

East Asian (EAS) AF: 0.875 AC: 3175 AN: 3630

South Asian (SAS) AF: 0.825 AC: 13584 AN: 16460

European-Finnish (FIN) AF: 0.877 AC: 242 AN: 276

Middle Eastern (MID) AF: 0.902 AC: 1462 AN: 1620

European-Non Finnish (NFE) AF: 0.839 AC: 639008 AN: 761888

Other (OTH) AF: 0.850 AC: 23194 AN: 27298

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

African (AFR) AF: 0.847 AC: 35179 AN: 41516

American (AMR) AF: 0.811 AC: 12406 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3138 AN: 3472

East Asian (EAS) AF: 0.882 AC: 4573 AN: 5182

South Asian (SAS) AF: 0.823 AC: 3966 AN: 4818

European-Finnish (FIN) AF: 0.912 AC: 9677 AN: 10606

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57836 AN: 68002

Other (OTH) AF: 0.857 AC: 1811 AN: 2114

Alfa AF: 0.851 Hom.: 90596

Bravo AF: 0.848

Asia WGS AF: 0.839 AC: 2920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.35
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1402752; hg19: chr3-44687300;