chr9-127439399-A-G

Variant names:

• chr9-127439399-A-G
• rs7869023
• NM_007135.3:c.328+3396A>G

Variant summary

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

The NM_007135.3(ZNF79):​c.328+3396A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,064 control chromosomes in the GnomAD database, including 28,474 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 0.61 (28474 hom., cov: 31)
• Consequence: ZNF79 NM_007135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 14 publications found

Genes affected

ZNF79 (HGNC:13153): (zinc finger protein 79) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [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 = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007135.3. 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
	ZNF79	NM_007135.3	MANE Select	c.328+3396A>G		intron	N/A	NP_009066.2	Q15937
	ZNF79	NM_001286696.2		c.256+3396A>G		intron	N/A	NP_001273625.1	F5H032
	ZNF79	NM_001286697.2		c.256+3396A>G		intron	N/A	NP_001273626.1	F5H032

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF79	ENST00000342483.5	TSL:1 MANE Select	c.328+3396A>G		intron	N/A	ENSP00000362446.4	Q15937
	ZNF79	ENST00000543471.6	TSL:2	c.256+3396A>G		intron	N/A	ENSP00000438418.1	F5H032
	ZNF79	ENST00000850856.1		c.256+3396A>G		intron	N/A	ENSP00000520944.1	F5H032

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92396 AN: 151946 Hom.: 28429 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.608 AC: 92493 AN: 152064 Hom.: 28474 Cov.: 31 AF XY: 0.608 AC XY: 45203 AN XY: 74330

African (AFR) AF: 0.641 AC: 26572 AN: 41462

American (AMR) AF: 0.629 AC: 9614 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2056 AN: 5164

South Asian (SAS) AF: 0.495 AC: 2388 AN: 4824

European-Finnish (FIN) AF: 0.686 AC: 7256 AN: 10574

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.600 AC: 40797 AN: 67982

Other (OTH) AF: 0.607 AC: 1280 AN: 2108

Alfa AF: 0.601 Hom.: 35534

Bravo AF: 0.606

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-0.078
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: rs7869023; hg19: chr9-130201678;