rs974230

Positions:

• chr9-112994095-T-C
• chr9-112994095-T-G

Variant summary

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

The NM_001101338.2(ZNF883):​c.*3025A>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 0.477 in 151,966 control chromosomes in the GnomAD database, including 19,093 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 0.48 (19093 hom., cov: 32)
• Consequence: ZNF883 NM_001101338.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

ZNF883 (HGNC:27271): (zinc finger protein 883) 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 located 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF883	NM_001101338.2	c.*3025A>G		3_prime_UTR_variant	5/5	ENST00000639662.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF883	ENST00000639662.2	c.*3025A>G		3_prime_UTR_variant	5/5		NM_001101338.2	P1
	ENST00000638823.1	n.309+4608A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000639196.1	n.1381+4026A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000692596.2	n.335+5596A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72465 AN: 151848 Hom.: 19066 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.477 AC: 72534 AN: 151966 Hom.: 19093 Cov.: 32 AF XY: 0.478 AC XY: 35469 AN XY: 74274

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.482

Alfa AF: 0.410 Hom.: 1726

Bravo AF: 0.496

Asia WGS AF: 0.667 AC: 2316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs974230; hg19: chr9-115756375; COSMIC: COSV71308947;