rs259677

Positions:

• chr6-37914230-A-G
• chr6-37914230-A-T

Variant summary

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

The NM_021943.3(ZFAND3):​c.72-15729A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,066 control chromosomes in the GnomAD database, including 31,244 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 0.63 (31244 hom., cov: 31)
• Consequence: ZFAND3 NM_021943.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFAND3	NM_021943.3	c.72-15729A>G		intron_variant		ENST00000287218.9	NP_068762.1
ZFAND3	NM_001410904.1	c.72-15729A>G		intron_variant			NP_001397833.1
ZFAND3	XM_011514790.3	c.72-15729A>G		intron_variant			XP_011513092.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFAND3	ENST00000287218.9	c.72-15729A>G		intron_variant		1	NM_021943.3	ENSP00000287218.4
ZFAND3	ENST00000373391.6	c.72-15729A>G		intron_variant		5		ENSP00000362489.2
ZFAND3	ENST00000474522.5	c.72-15729A>G		intron_variant		5		ENSP00000420240.1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96177 AN: 151948 Hom.: 31210 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.633 AC: 96257 AN: 152066 Hom.: 31244 Cov.: 31 AF XY: 0.627 AC XY: 46607 AN XY: 74332

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.594

Alfa AF: 0.626 Hom.: 3798

Bravo AF: 0.629

Asia WGS AF: 0.482 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.84

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: rs259677; hg19: chr6-37882006;