rs9332408

Variant names:

• chr17-67112871-T-C
• rs9332408
• NM_014877.4:c.3918+1453A>G

Variant summary

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

The NM_014877.4(HELZ):​c.3918+1453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,860 control chromosomes in the GnomAD database, including 19,162 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 0.49 (19162 hom., cov: 32)
• Consequence: HELZ NM_014877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 5 publications found

Genes affected

HELZ (HGNC:16878): (helicase with zinc finger) HELZ is a member of the superfamily I class of RNA helicases. RNA helicases alter the conformation of RNA by unwinding double-stranded regions, thereby altering the biologic activity of the RNA molecule and regulating access to other proteins (Wagner et al., 1999 [PubMed 10471385]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014877.4. 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
	HELZ	NM_014877.4	MANE Select	c.3918+1453A>G		intron	N/A	NP_055692.3
	HELZ	NM_001330447.2		c.3921+1453A>G		intron	N/A	NP_001317376.2	J3QS41

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELZ	ENST00000358691.10	TSL:1 MANE Select	c.3918+1453A>G		intron	N/A	ENSP00000351524.5	P42694-1
	HELZ	ENST00000580168.5	TSL:1	c.3921+1453A>G		intron	N/A	ENSP00000464512.1	J3QS41
	HELZ	ENST00000873042.1		c.4002+1453A>G		intron	N/A	ENSP00000543101.1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74552 AN: 151742 Hom.: 19160 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.491 AC: 74571 AN: 151860 Hom.: 19162 Cov.: 32 AF XY: 0.502 AC XY: 37256 AN XY: 74198

African (AFR) AF: 0.414 AC: 17126 AN: 41394

American (AMR) AF: 0.577 AC: 8812 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1530 AN: 3464

East Asian (EAS) AF: 0.879 AC: 4537 AN: 5164

South Asian (SAS) AF: 0.700 AC: 3362 AN: 4806

European-Finnish (FIN) AF: 0.551 AC: 5797 AN: 10520

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31810 AN: 67928

Other (OTH) AF: 0.491 AC: 1037 AN: 2110

Alfa AF: 0.482 Hom.: 23018

Bravo AF: 0.488

Asia WGS AF: 0.723 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.48
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs9332408; hg19: chr17-65108987;