rs10484396

Positions:

• chr6-27429419-T-C

Variant summary

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

The NR_144687.2(ZNF184):​n.571-19083A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

ZNF184 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF184	NR_144687.2	n.571-19083A>G		intron_variant, non_coding_transcript_variant
ZNF184	NR_144688.2	n.571-19083A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.635

Alfa AF: 0.621 Hom.: 11468

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484396; hg19: chr6-27397198;