rs1330691

Positions:

• chr9-113048337-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFP37	NM_003408.3	c.349+1025G>C		intron_variant		ENST00000374227.8	NP_003399.1
ZFP37	NM_001282515.2	c.394+1025G>C		intron_variant			NP_001269444.1
ZFP37	NM_001282518.2	c.352+1025G>C		intron_variant			NP_001269447.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFP37	ENST00000374227.8	c.349+1025G>C		intron_variant		1	NM_003408.3	ENSP00000363344
ZFP37	ENST00000555206.5	c.352+1025G>C		intron_variant		1		ENSP00000451310
ZFP37	ENST00000553380.1	c.394+1025G>C		intron_variant		2		ENSP00000452552	P1

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

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.573

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.25

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: rs1330691; hg19: chr9-115810617;