19-9688979-G-C

Variant names:

• chr19-9688979-G-C
• rs2009518
• NR_146444.1:n.2924C>G

Variant summary

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

The NR_146444.1(ZNF812P):​n.2924C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,014 control chromosomes in the GnomAD database, including 8,457 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 0.30 (8457 hom., cov: 32)
• Consequence: ZNF812P NR_146444.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 4 publications found

Genes affected

ZNF812P (HGNC:33242): (zinc finger protein 812, pseudogene)

ENSG00000291231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_146444.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF812P	NR_146444.1		n.2924C>G		non_coding_transcript_exon	Exon 4 of 4
	ZNF812P	NR_146445.1		n.2835C>G		non_coding_transcript_exon	Exon 3 of 3
	ZNF812P	NR_146446.1		n.2680C>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291231	ENST00000779066.1		n.380+5800C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45320 AN: 151894 Hom.: 8422 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.299 AC: 45416 AN: 152014 Hom.: 8457 Cov.: 32 AF XY: 0.300 AC XY: 22288 AN XY: 74300

African (AFR) AF: 0.513 AC: 21277 AN: 41440

American (AMR) AF: 0.355 AC: 5424 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3466

East Asian (EAS) AF: 0.0646 AC: 334 AN: 5172

South Asian (SAS) AF: 0.207 AC: 998 AN: 4820

European-Finnish (FIN) AF: 0.249 AC: 2621 AN: 10544

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13508 AN: 67978

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.113 Hom.: 167

Bravo AF: 0.316

Asia WGS AF: 0.209 AC: 729 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.26
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs2009518; hg19: chr19-9799655;