rs13195040

chr6-27446145-A-G

Variant summary

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

The NR_144687.2(ZNF184):n.570+10681T>C 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 0.0861 in 152,312 control chromosomes in the GnomAD database, including 709 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 0.086 (709 hom., cov: 32)
• Consequence: ZNF184 NR_144687.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

Genes affected

ZNF184 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF184	NR_144687.2	n.570+10681T>C		intron_variant, non_coding_transcript_variant
ZNF184	NR_144688.2	n.570+10681T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13117 AN: 152194 Hom.: 710 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0861 AC: 13121 AN: 152312 Hom.: 709 Cov.: 32 AF XY: 0.0804 AC XY: 5990 AN XY: 74482

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.0280

Gnomad4 EAS AF: 0.00404

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.0857

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0796 Hom.: 531

Bravo AF: 0.0916

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	3.3
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13195040; hg19: chr6-27413924;