16-73795371-A-C

Variant names:

• chr16-73795371-A-C
• rs427576
• NM_001386735.1:c.-1125+96280T>G

Variant summary

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

The NM_001386735.1(ZFHX3):​c.-1125+96280T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,912 control chromosomes in the GnomAD database, including 18,701 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 0.50 (18701 hom., cov: 32)
• Consequence: ZFHX3 NM_001386735.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

Genes affected

ZFHX3 (HGNC:777): (zinc finger homeobox 3) This gene encodes a transcription factor with multiple homeodomains and zinc finger motifs, and regulates myogenic and neuronal differentiation. The encoded protein suppresses expression of the alpha-fetoprotein gene by binding to an AT-rich enhancer motif. The protein has also been shown to negatively regulate c-Myb, and transactivate the cell cycle inhibitor cyclin-dependent kinase inhibitor 1A (also known as p21CIP1). This gene is reported to function as a tumor suppressor in several cancers, and sequence variants of this gene are also associated with atrial fibrillation. Multiple transcript variants expressed from alternate promoters and encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ENSG00000283457 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFHX3	NM_001386735.1	c.-1125+96280T>G		intron_variant	Intron 1 of 16		NP_001373664.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFHX3	ENST00000641206.2	c.-1608+96280T>G		intron_variant	Intron 1 of 17			ENSP00000493252.1
ENSG00000283457	ENST00000637695.1	n.261+1032A>C		intron_variant	Intron 1 of 3	5
ZFHX3	ENST00000641018.1	n.100+96280T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75129 AN: 151794 Hom.: 18681 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.495 AC: 75211 AN: 151912 Hom.: 18701 Cov.: 32 AF XY: 0.495 AC XY: 36753 AN XY: 74228

African (AFR) AF: 0.537 AC: 22236 AN: 41410

American (AMR) AF: 0.522 AC: 7972 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1711 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2616 AN: 5146

South Asian (SAS) AF: 0.616 AC: 2970 AN: 4820

European-Finnish (FIN) AF: 0.413 AC: 4353 AN: 10540

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31829 AN: 67946

Other (OTH) AF: 0.500 AC: 1053 AN: 2108

Alfa AF: 0.481 Hom.: 35600

Bravo AF: 0.502

Asia WGS AF: 0.566 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.94
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs427576; hg19: chr16-73829270;