rs7869023

Positions:

• chr9-127439399-A-G
• chr9-127439399-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

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 = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF79	NM_007135.3	c.328+3396A>G		intron_variant		ENST00000342483.5	NP_009066.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF79	ENST00000342483.5	c.328+3396A>G		intron_variant		1	NM_007135.3	ENSP00000362446.4
ZNF79	ENST00000543471.5	c.256+3396A>G		intron_variant		2		ENSP00000438418.1
ZNF79	ENST00000612342.4	c.256+3396A>G		intron_variant		2		ENSP00000478201.1
ZNF79	ENST00000617266.2	c.-74-4630A>G		intron_variant		3		ENSP00000484833.1

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

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.607

Alfa AF: 0.598 Hom.: 26786

Bravo AF: 0.606

Asia WGS AF: 0.482 AC: 1675 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	1.7
DANN	Benign	0.69

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: rs7869023; hg19: chr9-130201678;