rs10484396

Variant names:

• chr6-27429419-T-C
• rs10484396
• NR_144687.2:n.571-19083A>G

Variant summary

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

The NR_144687.2(ZNF184):​n.571-19083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,958 control chromosomes in the GnomAD database, including 27,230 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 0.59 (27230 hom., cov: 32)
• Consequence: ZNF184 NR_144687.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF184	NR_144687.2	n.571-19083A>G		intron_variant	Intron 5 of 8
ZNF184	NR_144688.2	n.571-19083A>G		intron_variant	Intron 5 of 8

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90350 AN: 151840 Hom.: 27215 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.595 AC: 90401 AN: 151958 Hom.: 27230 Cov.: 32 AF XY: 0.596 AC XY: 44218 AN XY: 74252

African (AFR) AF: 0.499 AC: 20673 AN: 41424

American (AMR) AF: 0.651 AC: 9952 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2709 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2971 AN: 5164

South Asian (SAS) AF: 0.723 AC: 3484 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5675 AN: 10556

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42896 AN: 67936

Other (OTH) AF: 0.635 AC: 1340 AN: 2110

Alfa AF: 0.621 Hom.: 13865

Bravo AF: 0.597

Asia WGS AF: 0.646 AC: 2246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.2
DANN	Benign	0.44
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs10484396; hg19: chr6-27397198;