rs918376480

Variant names:

• chr9-96417699-G-T
• rs918376480
• NM_153695.4:c.334C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-96417699-G-T
• chr9-96417699-G-A

Variant summary

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

The NM_153695.4(ZNF367):​c.334C>A​(p.Pro112Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,165,926 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00087 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0013 (1 hom.)
• Consequence: ZNF367 NM_153695.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.440
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.013578504).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153695.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF367	NM_153695.4	MANE Select	c.334C>A	p.Pro112Thr	missense	Exon 1 of 5	NP_710162.1	Q7RTV3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF367	ENST00000375256.5	TSL:1 MANE Select	c.334C>A	p.Pro112Thr	missense	Exon 1 of 5	ENSP00000364405.4	Q7RTV3-1

Frequencies

GnomAD3 genomes AF: 0.000873 AC: 131 AN: 150084 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000389

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000597

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000401

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00150

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00281 AC: 1 AN: 356 AF XY: 0.00431

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00388

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00131 AC: 1334 AN: 1015740 Hom.: 1 Cov.: 19 AF XY: 0.00128 AC XY: 617 AN XY: 481194

African (AFR) AF: 0.0000475 AC: 1 AN: 21036

American (AMR) AF: 0.000670 AC: 5 AN: 7460

Ashkenazi Jewish (ASJ) AF: 0.000157 AC: 2 AN: 12726

East Asian (EAS) AF: 0.00 AC: 0 AN: 24008

South Asian (SAS) AF: 0.000162 AC: 3 AN: 18544

European-Finnish (FIN) AF: 0.000484 AC: 10 AN: 20656

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2710

European-Non Finnish (NFE) AF: 0.00146 AC: 1266 AN: 868272

Other (OTH) AF: 0.00117 AC: 47 AN: 40328

GnomAD4 genome AF: 0.000872 AC: 131 AN: 150186 Hom.: 0 Cov.: 33 AF XY: 0.000914 AC XY: 67 AN XY: 73292

African (AFR) AF: 0.000388 AC: 16 AN: 41252

American (AMR) AF: 0.000596 AC: 9 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.000290 AC: 1 AN: 3446

East Asian (EAS) AF: 0.00 AC: 0 AN: 5094

South Asian (SAS) AF: 0.00 AC: 0 AN: 4814

European-Finnish (FIN) AF: 0.000401 AC: 4 AN: 9978

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 284

European-Non Finnish (NFE) AF: 0.00150 AC: 101 AN: 67232

Other (OTH) AF: 0.00 AC: 0 AN: 2088

Alfa AF: 0.00140 Hom.: 0

Bravo AF: 0.000960

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.55	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	19
DANN	Benign	0.94
DEOGEN2	Benign	0.022	T
Eigen	Benign	-0.099
Eigen_PC	Benign	-0.058
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.37	T
M_CAP	Pathogenic	0.37	D
MetaRNN	Benign	0.014	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.90	L
PhyloP100		0.44
PrimateAI	Pathogenic	0.87	D
PROVEAN	Benign	0.24	N
REVEL	Benign	0.051
Sift	Uncertain	0.015	D
Sift4G	Benign	0.33	T
Polyphen		0.60	P
Vest4		0.17
MVP		0.093
MPC		1.2
ClinPred		0.045	T
GERP RS		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1
Varity_R		0.070
gMVP		0.34
Mutation Taster		=90/10	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs918376480; hg19: chr9-99179981;