rs2025151

Positions:

• chr9-96399230-C-G

Variant summary

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

The NM_153695.4(ZNF367):​c.421-916G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,726 control chromosomes in the GnomAD database, including 8,490 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 0.29 (8490 hom., cov: 31)
• Consequence: ZNF367 NM_153695.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

ZNF367 (HGNC:18320): (zinc finger protein 367) Enables DNA-binding transcription factor activity. Acts upstream of or within regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF367	NM_153695.4	c.421-916G>C		intron_variant		ENST00000375256.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF367	ENST00000375256.5	c.421-916G>C		intron_variant		1	NM_153695.4	P1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43469 AN: 151608 Hom.: 8439 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.287 AC: 43580 AN: 151726 Hom.: 8490 Cov.: 31 AF XY: 0.279 AC XY: 20715 AN XY: 74140

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.259

Alfa AF: 0.261 Hom.: 801

Bravo AF: 0.296

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.69
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025151; hg19: chr9-99161512;