rs76439045

Variant names:

• chr6-27443950-A-C
• rs76439045
• NR_144687.2:n.570+12876T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-27443950-A-C
• chr6-27443950-A-T

Variant summary

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

The NR_144687.2(ZNF184):​n.570+12876T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 151,552 control chromosomes in the GnomAD database, including 66 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 0.012 (66 hom., cov: 31)
• Consequence: ZNF184 NR_144687.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

Genes affected

ZNF184 (HGNC:12975): (zinc finger protein 184) The protein encoded by this gene is predicted to be a Kruppel C2H2-type zinc-finger protein family member. Sequence analysis predicts that the protein contains two Kruppel associated box (KRAB) boxes in the N-terminus and highly conserved zinc finger motifs at the C-terminus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2016]

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 = 0.0972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF184	NR_144687.2	n.570+12876T>G		intron_variant	Intron 5 of 8
ZNF184	NR_144688.2	n.570+12876T>G		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0119 AC: 1796 AN: 151438 Hom.: 65 Cov.: 31

Gnomad AFR AF: 0.00175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0152

Gnomad FIN AF: 0.00486

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00421

Gnomad OTH AF: 0.00913

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

GnomAD4 genome AF: 0.0119 AC: 1801 AN: 151552 Hom.: 66 Cov.: 31 AF XY: 0.0137 AC XY: 1013 AN XY: 74048

Gnomad4 AFR AF: 0.00175

Gnomad4 AMR AF: 0.0497

Gnomad4 ASJ AF: 0.00116

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0154

Gnomad4 FIN AF: 0.00486

Gnomad4 NFE AF: 0.00421

Gnomad4 OTH AF: 0.00904

Alfa AF: 0.00423 Hom.: 3

Bravo AF: 0.0138

Asia WGS AF: 0.0370 AC: 129 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	1.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76439045; hg19: chr6-27411729;