chr9-96399230-C-G

Variant names:

• chr9-96399230-C-G
• rs2025151
• NM_153695.4:c.421-916G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF367	NM_153695.4	c.421-916G>C		intron_variant	Intron 1 of 4	ENST00000375256.5	NP_710162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF367	ENST00000375256.5	c.421-916G>C		intron_variant	Intron 1 of 4	1	NM_153695.4	ENSP00000364405.4

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

African (AFR) AF: 0.562 AC: 23197 AN: 41274

American (AMR) AF: 0.174 AC: 2648 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3468

East Asian (EAS) AF: 0.0297 AC: 153 AN: 5156

South Asian (SAS) AF: 0.152 AC: 732 AN: 4822

European-Finnish (FIN) AF: 0.169 AC: 1775 AN: 10514

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.200 AC: 13575 AN: 67956

Other (OTH) AF: 0.259 AC: 542 AN: 2096

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
PhyloP100		-0.25
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: rs2025151; hg19: chr9-99161512;