rs974230

Variant names:

• chr9-112994095-T-C
• rs974230
• NM_001101338.2:c.*3025A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000291094 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF883	NM_001101338.2	c.*3025A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000639662.2	NP_001094808.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF883	ENST00000639662.2	c.*3025A>G		3_prime_UTR_variant	Exon 5 of 5	6	NM_001101338.2	ENSP00000516482.1

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

African (AFR) AF: 0.666 AC: 27655 AN: 41498

American (AMR) AF: 0.455 AC: 6942 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3466

East Asian (EAS) AF: 0.813 AC: 4196 AN: 5160

South Asian (SAS) AF: 0.560 AC: 2696 AN: 4814

European-Finnish (FIN) AF: 0.324 AC: 3413 AN: 10548

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24803 AN: 67896

Other (OTH) AF: 0.482 AC: 1016 AN: 2108

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

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