9-96417727-C-T

Variant names:

• chr9-96417727-C-T
• rs1288451675
• NM_153695.4:c.306G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_153695.4(ZNF367):​c.306G>A​(p.Glu102Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000327 in 1,223,240 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: ZNF367 NM_153695.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.874
• Publications: 0 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 -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BP7: Synonymous conserved (PhyloP=0.874 with no splicing effect.

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.306G>A	p.Glu102Glu	synonymous	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.306G>A	p.Glu102Glu	synonymous	Exon 1 of 5	ENSP00000364405.4	Q7RTV3-1

Frequencies

GnomAD3 genomes AF: 0.00000663 AC: 1 AN: 150772 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000148

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000280 AC: 3 AN: 1072468 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 507080

African (AFR) AF: 0.00 AC: 0 AN: 22588

American (AMR) AF: 0.00 AC: 0 AN: 8200

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14036

East Asian (EAS) AF: 0.00 AC: 0 AN: 26204

South Asian (SAS) AF: 0.00 AC: 0 AN: 19618

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21894

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2892

European-Non Finnish (NFE) AF: 0.00000328 AC: 3 AN: 913902

Other (OTH) AF: 0.00 AC: 0 AN: 43134

GnomAD4 genome AF: 0.00000663 AC: 1 AN: 150772 Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1 AN XY: 73590

African (AFR) AF: 0.00 AC: 0 AN: 41228

American (AMR) AF: 0.00 AC: 0 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3460

East Asian (EAS) AF: 0.00 AC: 0 AN: 5158

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10104

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.0000148 AC: 1 AN: 67570

Other (OTH) AF: 0.00 AC: 0 AN: 2078

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	12
DANN	Uncertain	0.98
PhyloP100		0.87

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: rs1288451675; hg19: chr9-99180009;