Variant 10-94545972-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018063.5(HELLS):c.31+20T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 1,554,014 control chromosomes in the GnomAD database, including 167,980 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 17756 hom., cov: 31)

Exomes 𝑓: 0.46 ( 150224 hom. )

Consequence

HELLS
NM_018063.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.432

Variant links:

Genes affected

HELLS (HGNC:4861): (helicase, lymphoid specific) This gene encodes a lymphoid-specific helicase. Other helicases function in processes involving DNA strand separation, including replication, repair, recombination, and transcription. This protein is thought to be involved with cellular proliferation and may play a role in leukemogenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jan 2014]

HELLS links:

HELLS (HGNC:):

HELLS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 10-94545972-T-C is Benign according to our data. Variant chr10-94545972-T-C is described in ClinVar as [Benign]. Clinvar id is 1166855.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HELLS	NM_018063.5 linkuse as main transcript	c.31+20T>C		intron_variant		ENST00000348459.10	NP_060533.2	Q9NRZ9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HELLS	ENST00000348459.10 linkuse as main transcript	c.31+20T>C		intron_variant		1	NM_018063.5	ENSP00000239027.7		Q9NRZ9-1

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72322

AN:

151760

Hom.:

17744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.779

Gnomad SAS

AF:

0.592

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.461

GnomAD3 exomes

AF:

0.474

AC:

74575

AN:

157352

Hom.:

18708

AF XY:

0.480

AC XY:

40083

AN XY:

83444

show subpopulations

Gnomad AFR exome

AF:

0.565

Gnomad AMR exome

AF:

0.364

Gnomad ASJ exome

AF:

0.433

Gnomad EAS exome

AF:

0.783

Gnomad SAS exome

AF:

0.574

Gnomad FIN exome

AF:

0.363

Gnomad NFE exome

AF:

0.443

Gnomad OTH exome

AF:

0.456

GnomAD4 exome

AF:

0.457

AC:

640958

AN:

1402136

Hom.:

150224

Cov.:

AF XY:

0.459

AC XY:

317852

AN XY:

691912

show subpopulations

Gnomad4 AFR exome

AF:

0.568

Gnomad4 AMR exome

AF:

0.363

Gnomad4 ASJ exome

AF:

0.426

Gnomad4 EAS exome

AF:

0.775

Gnomad4 SAS exome

AF:

0.572

Gnomad4 FIN exome

AF:

0.368

Gnomad4 NFE exome

AF:

0.442

Gnomad4 OTH exome

AF:

0.471

GnomAD4 genome

AF:

0.477

AC:

72375

AN:

151878

Hom.:

17756

Cov.:

AF XY:

0.477

AC XY:

35400

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.557

Gnomad4 AMR

AF:

0.393

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.779

Gnomad4 SAS

AF:

0.593

Gnomad4 FIN

AF:

0.367

Gnomad4 NFE

AF:

0.437

Gnomad4 OTH

AF:

0.464

Alfa

AF:

0.434

Hom.:

14652

Bravo

AF:

0.481

Asia WGS

AF:

0.681

AC:

2371

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Immunodeficiency-centromeric instability-facial anomalies syndrome 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.5

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over