17-67150713-C-T

Position:

• chr17-67150713-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014877.4(HELZ):​c.2356+333G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,056 control chromosomes in the GnomAD database, including 28,736 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 0.60 (28736 hom., cov: 32)
• Consequence: HELZ NM_014877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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]

HELZ (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HELZ	NM_014877.4	c.2356+333G>A		intron_variant		ENST00000358691.10	NP_055692.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HELZ	ENST00000358691.10	c.2356+333G>A		intron_variant		1	NM_014877.4	ENSP00000351524.5
HELZ	ENST00000580168.5	c.2359+333G>A		intron_variant		1		ENSP00000464512.1
HELZ	ENST00000579953.5	n.2359+333G>A		intron_variant		2		ENSP00000463727.1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91260 AN: 151936 Hom.: 28706 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.601 AC: 91335 AN: 152056 Hom.: 28736 Cov.: 32 AF XY: 0.610 AC XY: 45339 AN XY: 74320

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.571

Alfa AF: 0.534 Hom.: 2697

Bravo AF: 0.608

Asia WGS AF: 0.753 AC: 2619 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.53

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: rs2363846; hg19: chr17-65146829;