rs9470794

Variant names:

• chr6-38139068-T-C
• rs9470794
• NM_021943.3:c.530-13167T>C

Variant summary

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

The NM_021943.3(ZFAND3):​c.530-13167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,196 control chromosomes in the GnomAD database, including 1,330 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 0.12 (1330 hom., cov: 32)
• Consequence: ZFAND3 NM_021943.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 85 publications found

Genes affected

ZFAND3 (HGNC:18019): (zinc finger AN1-type containing 3) Predicted to enable DNA binding activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

LOC124901314 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFAND3	NM_021943.3	c.530-13167T>C		intron_variant	Intron 5 of 5	ENST00000287218.9	NP_068762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFAND3	ENST00000287218.9	c.530-13167T>C		intron_variant	Intron 5 of 5	1	NM_021943.3	ENSP00000287218.4
ZFAND3	ENST00000373391.6	c.464-13167T>C		intron_variant	Intron 4 of 4	5		ENSP00000362489.2
ZFAND3	ENST00000373389.5	c.458-3191T>C		intron_variant	Intron 4 of 4	5		ENSP00000362487.5
ZFAND3	ENST00000440482.2	n.212-13167T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18062 AN: 152078 Hom.: 1326 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0468

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.119 AC: 18081 AN: 152196 Hom.: 1330 Cov.: 32 AF XY: 0.118 AC XY: 8791 AN XY: 74414

African (AFR) AF: 0.166 AC: 6867 AN: 41490

American (AMR) AF: 0.106 AC: 1615 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1477 AN: 5172

South Asian (SAS) AF: 0.119 AC: 576 AN: 4824

European-Finnish (FIN) AF: 0.0468 AC: 497 AN: 10614

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0925 AC: 6290 AN: 68006

Other (OTH) AF: 0.142 AC: 301 AN: 2116

Alfa AF: 0.103 Hom.: 2432

Bravo AF: 0.128

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-2.4
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: rs9470794; hg19: chr6-38106844;