9-72360685-C-G

Variant names:

• chr9-72360685-C-G
• rs1842071696
• NM_001102420.3:c.94G>C

Variant summary

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

The NM_001102420.3(ZFAND5):​c.94G>C​(p.Val32Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZFAND5 NM_001102420.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.08
• Publications: 0 publications found

Genes affected

ZFAND5 (HGNC:13008): (zinc finger AN1-type containing 5) Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to act upstream of or within several processes, including face development; fibroblast migration; and platelet-derived growth factor receptor signaling pathway. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LINC01504 (HGNC:51185): (long intergenic non-protein coding RNA 1504)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102420.3. 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
	ZFAND5	NM_001102420.3	MANE Select	c.94G>C	p.Val32Leu	missense	Exon 3 of 7	NP_001095890.1	O76080
	ZFAND5	NM_001102421.3		c.94G>C	p.Val32Leu	missense	Exon 2 of 6	NP_001095891.1	O76080
	ZFAND5	NM_001278243.2		c.94G>C	p.Val32Leu	missense	Exon 3 of 7	NP_001265172.1	O76080

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAND5	ENST00000376962.10	TSL:1 MANE Select	c.94G>C	p.Val32Leu	missense	Exon 3 of 7	ENSP00000366161.5	O76080
	ZFAND5	ENST00000376960.8	TSL:1	c.94G>C	p.Val32Leu	missense	Exon 2 of 6	ENSP00000366159.4	O76080
	ZFAND5	ENST00000237937.7	TSL:5	c.94G>C	p.Val32Leu	missense	Exon 2 of 6	ENSP00000237937.3	O76080

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

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	Pathogenic	0.67
BayesDel_addAF	Benign	-0.050	T
BayesDel_noAF	Benign	-0.31
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Benign	0.20	T
Eigen	Pathogenic	0.79
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.96	D
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.58	D
MetaSVM	Benign	-0.71	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		6.1
PrimateAI	Pathogenic	0.89	D
PROVEAN	Benign	-1.6	N
REVEL	Benign	0.27
Sift	Uncertain	0.021	D
Sift4G	Benign	0.19	T
Polyphen		1.0	D
Vest4		0.45
MutPred		0.47		Gain of ubiquitination at K35 (P = 0.0804)
MVP		0.068
MPC		1.5
ClinPred		0.96	D
GERP RS		6.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.7
Varity_R		0.34
gMVP		0.57
Mutation Taster		=73/27	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

dbSNP: rs1842071696; hg19: chr9-74975601;