9-72355992-C-T

Variant names:

• chr9-72355992-C-T
• rs781212359
• NM_001102420.3:c.603G>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001102420.3(ZFAND5):​c.603G>A​(p.Glu201Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ZFAND5 NM_001102420.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP7: Synonymous conserved (PhyloP=0.502 with no splicing effect.

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.603G>A	p.Glu201Glu	synonymous	Exon 7 of 7	NP_001095890.1	O76080
	ZFAND5	NM_001102421.3		c.603G>A	p.Glu201Glu	synonymous	Exon 6 of 6	NP_001095891.1	O76080
	ZFAND5	NM_001278243.2		c.603G>A	p.Glu201Glu	synonymous	Exon 7 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.603G>A	p.Glu201Glu	synonymous	Exon 7 of 7	ENSP00000366161.5	O76080
	ZFAND5	ENST00000376960.8	TSL:1	c.603G>A	p.Glu201Glu	synonymous	Exon 6 of 6	ENSP00000366159.4	O76080
	ZFAND5	ENST00000471197.1	TSL:1	n.516G>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00000400 AC: 1 AN: 249802 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000883

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.46
PhyloP100		0.50

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: rs781212359; hg19: chr9-74970908;