XR_007061981.1:n.2083-393T>C

Variant names:

• chr10-43490979-T-C
• rs3124205
• XR_007061981.1:n.2083-393T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061981.1(ZNF487):​n.2083-393T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 133,520 control chromosomes in the GnomAD database, including 17,938 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 0.50 (17938 hom., cov: 23)
• Consequence: ZNF487 XR_007061981.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 1 publications found

Genes affected

ZNF487 (HGNC:23488): (zinc finger protein 487) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.498 AC: 66481 AN: 133450 Hom.: 17928 Cov.: 23

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.498 AC: 66490 AN: 133520 Hom.: 17938 Cov.: 23 AF XY: 0.499 AC XY: 32185 AN XY: 64452

African (AFR) AF: 0.222 AC: 7383 AN: 33308

American (AMR) AF: 0.612 AC: 8375 AN: 13682

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1603 AN: 3322

East Asian (EAS) AF: 0.732 AC: 3387 AN: 4630

South Asian (SAS) AF: 0.509 AC: 2184 AN: 4290

European-Finnish (FIN) AF: 0.579 AC: 4521 AN: 7814

Middle Eastern (MID) AF: 0.548 AC: 136 AN: 248

European-Non Finnish (NFE) AF: 0.587 AC: 37255 AN: 63474

Other (OTH) AF: 0.542 AC: 1007 AN: 1858

Alfa AF: 0.477 Hom.: 1784

Bravo AF: 0.462

Asia WGS AF: 0.551 AC: 1825 AN: 3308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.8
DANN	Benign	0.49
PhyloP100		-0.56
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: rs3124205; hg19: chr10-43986427;