rs10484578

chr6-35278542-A-Gchr6-35278542-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003427.5(ZNF76):c.-96-2514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,200 control chromosomes in the GnomAD database, including 22,762 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 0.49 (22762 hom., cov: 33)
• Consequence: ZNF76 NM_003427.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

ZNF76 (HGNC:13149): (zinc finger protein 76) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF76	NM_003427.5	c.-96-2514A>G		intron_variant		ENST00000373953.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF76	ENST00000373953.8	c.-96-2514A>G		intron_variant		1	NM_003427.5	P1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74709 AN: 152082 Hom.: 22753 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.491 AC: 74705 AN: 152200 Hom.: 22762 Cov.: 33 AF XY: 0.493 AC XY: 36642 AN XY: 74384

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.470

Alfa AF: 0.611 Hom.: 9262

Bravo AF: 0.462

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.33

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: rs10484578; hg19: chr6-35246319;