rs17589516

chr6-38068644-A-G

Variant summary

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

The NM_021943.3(ZFAND3):c.295+6869A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 152,288 control chromosomes in the GnomAD database, including 452 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 0.065 (452 hom., cov: 32)
• Consequence: ZFAND3 NM_021943.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.093 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFAND3	NM_021943.3	c.295+6869A>G		intron_variant		ENST00000287218.9
ZFAND3	NM_001410904.1	c.295+6869A>G		intron_variant
ZFAND3	XM_011514790.3	c.295+6869A>G		intron_variant
ZFAND3	XM_017011171.3	c.247+6869A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFAND3	ENST00000287218.9	c.295+6869A>G		intron_variant		1	NM_021943.3	P1
ZFAND3	ENST00000373389.5	c.224+6869A>G		intron_variant		5
ZFAND3	ENST00000373391.6	c.295+6869A>G		intron_variant		5
ZFAND3	ENST00000474522.5	c.388+6869A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9978 AN: 152170 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0655 AC: 9972 AN: 152288 Hom.: 452 Cov.: 32 AF XY: 0.0636 AC XY: 4734 AN XY: 74454

Gnomad4 AFR AF: 0.0150

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.0635

Gnomad4 FIN AF: 0.0643

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0962 Hom.: 1481

Bravo AF: 0.0624

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.60
Dann	Benign	0.80

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: rs17589516; hg19: chr6-38036420;