NM_021943.3:c.11C>A

Variant names:

• chr6-37819956-C-A
• NM_021943.3:c.11C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_021943.3(ZFAND3):​c.11C>A​(p.Ala4Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZFAND3 NM_021943.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.53
• Publications: 0 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11725509).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021943.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAND3	NM_021943.3	MANE Select	c.11C>A	p.Ala4Asp	missense	Exon 1 of 6	NP_068762.1	Q9H8U3
	ZFAND3	NM_001410904.1		c.11C>A	p.Ala4Asp	missense	Exon 1 of 5	NP_001397833.1	E2QRF5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAND3	ENST00000287218.9	TSL:1 MANE Select	c.11C>A	p.Ala4Asp	missense	Exon 1 of 6	ENSP00000287218.4	Q9H8U3
	ZFAND3	ENST00000894325.1		c.11C>A	p.Ala4Asp	missense	Exon 1 of 6	ENSP00000564384.1
	ZFAND3	ENST00000373391.6	TSL:5	c.11C>A	p.Ala4Asp	missense	Exon 1 of 5	ENSP00000362489.2	E2QRF5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1071464 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 508778

African (AFR) AF: 0.00 AC: 0 AN: 22232

American (AMR) AF: 0.00 AC: 0 AN: 7850

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13448

East Asian (EAS) AF: 0.00 AC: 0 AN: 25014

South Asian (SAS) AF: 0.00 AC: 0 AN: 20974

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21070

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2832

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 915546

Other (OTH) AF: 0.00 AC: 0 AN: 42498

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Uncertain	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0094	T
Eigen	Benign	-0.27
Eigen_PC	Benign	-0.14
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.83	T
M_CAP	Uncertain	0.26	D
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		4.5
PrimateAI	Pathogenic	0.92	D
PROVEAN	Benign	-0.78	N
REVEL	Benign	0.058
Sift	Uncertain	0.010	D
Sift4G	Uncertain	0.040	D
Polyphen		0.18	B
Vest4		0.31
MutPred		0.16		Loss of catalytic residue at A4 (P = 0.0098)
MVP		0.043
MPC		0.42
ClinPred		0.85	D
GERP RS		3.0
PromoterAI		0.049	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.50
gMVP		0.41
Mutation Taster		=76/24	polymorphism

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

hg19: chr6-37787732;