rs7500906

Positions:

• chr16-49762920-G-A
• chr16-49762920-G-C

Variant summary

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

The NM_001379286.1(ZNF423):​c.100+26567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,090 control chromosomes in the GnomAD database, including 23,792 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 0.55 (23792 hom., cov: 33)
• Consequence: ZNF423 NM_001379286.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

ZNF423 (HGNC:16762): (zinc finger protein 423) The protein encoded by this gene is a nuclear protein that belongs to the family of Kruppel-like C2H2 zinc finger proteins. It functions as a DNA-binding transcription factor by using distinct zinc fingers in different signaling pathways. Thus, it is thought that this gene may have multiple roles in signal transduction during development. Mutations in this gene are associated with nephronophthisis-14 and Joubert syndrome-19. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF423	NM_001379286.1	c.100+26567C>T		intron_variant		ENST00000563137.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF423	ENST00000563137.7	c.100+26567C>T		intron_variant		5	NM_001379286.1	P1

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83072 AN: 151972 Hom.: 23752 Cov.: 33

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.547 AC: 83160 AN: 152090 Hom.: 23792 Cov.: 33 AF XY: 0.548 AC XY: 40697 AN XY: 74326

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.528

Alfa AF: 0.397 Hom.: 1484

Bravo AF: 0.563

Asia WGS AF: 0.478 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.52

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: rs7500906; hg19: chr16-49796831;