8-143256883-G-A

Variant names:

• chr8-143256883-G-A
• rs10090179
• NM_173832.6:c.*901-2892G>A

Variant summary

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

The NM_173832.6(ZFP41):​c.*901-2892G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,108 control chromosomes in the GnomAD database, including 13,781 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 0.39 (13781 hom., cov: 33)
• Consequence: ZFP41 NM_173832.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 12 publications found

Genes affected

ZFP41 (HGNC:26786): (ZFP41 zinc finger protein) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000264668 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173832.6. 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
	ZFP41	NM_173832.6	MANE Select	c.*901-2892G>A		intron	N/A	NP_776193.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP41	ENST00000330701.7	TSL:2 MANE Select	c.*901-2892G>A		intron	N/A	ENSP00000327427.6
	ENSG00000264668	ENST00000522452.2	TSL:1	c.*900+5543G>A		intron	N/A	ENSP00000428966.3

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58971 AN: 151992 Hom.: 13762 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.388 AC: 59006 AN: 152108 Hom.: 13781 Cov.: 33 AF XY: 0.402 AC XY: 29882 AN XY: 74356

African (AFR) AF: 0.129 AC: 5366 AN: 41498

American (AMR) AF: 0.562 AC: 8592 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3472

East Asian (EAS) AF: 0.690 AC: 3576 AN: 5184

South Asian (SAS) AF: 0.626 AC: 3017 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5684 AN: 10558

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30135 AN: 67976

Other (OTH) AF: 0.401 AC: 847 AN: 2114

Alfa AF: 0.417 Hom.: 39630

Bravo AF: 0.376

Asia WGS AF: 0.618 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.55
PhyloP100		0.10
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs10090179; hg19: chr8-144339053;