rs1330691

Variant names:

• chr9-113048337-C-G
• rs1330691
• NM_003408.3:c.349+1025G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003408.3(ZFP37):​c.349+1025G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,848 control chromosomes in the GnomAD database, including 23,942 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 0.56 (23942 hom., cov: 31)
• Consequence: ZFP37 NM_003408.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 2 publications found

Genes affected

ZFP37 (HGNC:12863): (ZFP37 zinc finger protein) This gene encodes a transcription factor that belongs to a large family of zinc finger proteins. A similar protein in mouse is thought to play a role in regulating the structures of the nucleolus and centromere in neurons. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003408.3. 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
	ZFP37	NM_003408.3	MANE Select	c.349+1025G>C		intron	N/A	NP_003399.1	Q9Y6Q3-1
	ZFP37	NM_001282515.2		c.394+1025G>C		intron	N/A	NP_001269444.1	Q9Y6Q3-2
	ZFP37	NM_001282518.2		c.352+1025G>C		intron	N/A	NP_001269447.1	Q9Y6Q3-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP37	ENST00000374227.8	TSL:1 MANE Select	c.349+1025G>C		intron	N/A	ENSP00000363344.3	Q9Y6Q3-1
	ZFP37	ENST00000555206.5	TSL:1	c.352+1025G>C		intron	N/A	ENSP00000451310.1	Q9Y6Q3-3
	ZFP37	ENST00000553380.1	TSL:2	c.394+1025G>C		intron	N/A	ENSP00000452552.1	Q9Y6Q3-2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84824 AN: 151730 Hom.: 23912 Cov.: 31

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.559 AC: 84910 AN: 151848 Hom.: 23942 Cov.: 31 AF XY: 0.565 AC XY: 41908 AN XY: 74216

African (AFR) AF: 0.543 AC: 22497 AN: 41412

American (AMR) AF: 0.594 AC: 9074 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2036 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4098 AN: 5164

South Asian (SAS) AF: 0.607 AC: 2909 AN: 4796

European-Finnish (FIN) AF: 0.588 AC: 6194 AN: 10532

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36244 AN: 67894

Other (OTH) AF: 0.573 AC: 1204 AN: 2102

Alfa AF: 0.549 Hom.: 2848

Bravo AF: 0.555

Asia WGS AF: 0.680 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.25
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

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: rs1330691; hg19: chr9-115810617;