19-20930142-A-G

Variant names:

• chr19-20930142-A-G
• rs10454111
• NM_003429.5:c.4-3882A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_003429.5(ZNF85):​c.4-3882A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000544 in 145,248 control chromosomes in the GnomAD database, including 1 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 0.00054 (1 hom., cov: 29)
• Consequence: ZNF85 NM_003429.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 2 publications found

Genes affected

ZNF85 (HGNC:13160): (zinc finger protein 85) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000298806 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003429.5. 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
	ZNF85	NM_003429.5	MANE Select	c.4-3882A>G		intron	N/A	NP_003420.2
	ZNF85	NM_001256171.2		c.4-3882A>G		intron	N/A	NP_001243100.1
	ZNF85	NM_001256173.2		c.-62-4807A>G		intron	N/A	NP_001243102.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF85	ENST00000328178.13	TSL:1 MANE Select	c.4-3882A>G		intron	N/A	ENSP00000329793.7
	ZNF85	ENST00000300540.7	TSL:1	c.4-3882A>G		intron	N/A	ENSP00000300540.2
	ZNF85	ENST00000596476.1	TSL:1	c.-93-3882A>G		intron	N/A	ENSP00000469496.1

Frequencies

GnomAD3 genomes AF: 0.000537 AC: 78 AN: 145148 Hom.: 1 Cov.: 29

Gnomad AFR AF: 0.000632

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000276

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000575

Gnomad OTH AF: 0.000504

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

GnomAD4 genome AF: 0.000544 AC: 79 AN: 145248 Hom.: 1 Cov.: 29 AF XY: 0.000653 AC XY: 46 AN XY: 70466

African (AFR) AF: 0.000631 AC: 25 AN: 39648

American (AMR) AF: 0.000276 AC: 4 AN: 14504

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3418

East Asian (EAS) AF: 0.00 AC: 0 AN: 5060

South Asian (SAS) AF: 0.00 AC: 0 AN: 4586

European-Finnish (FIN) AF: 0.00113 AC: 10 AN: 8840

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.000590 AC: 39 AN: 66070

Other (OTH) AF: 0.000500 AC: 1 AN: 2002

Alfa AF: 0.00804 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.79
PhyloP100		-0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10454111; hg19: chr19-21112948;