Genetic Variant HELQ:c.1393-47C>T (chr4-83446133-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_133636.5(HELQ):c.1393-47C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 1,263,222 control chromosomes in the GnomAD database, including 165,805 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 0.50 ( 19610 hom., cov: 32)

Exomes 𝑓: 0.51 ( 146195 hom. )

Consequence

HELQ
NM_133636.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.596

Publications

12 publications found

Variant links:

Genes affected

HELQ (HGNC:18536): (helicase, POLQ like) HEL308 is a single-stranded DNA-dependent ATPase and DNA helicase (Marini and Wood, 2002 [PubMed 11751861]).[supplied by OMIM, Mar 2008]

HELQ links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133636.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HELQ	NM_133636.5	MANE Select	c.1393-47C>T	intron	N/A	NP_598375.3	Q8TDG4-1
HELQ	NM_001297755.2		c.1192-47C>T	intron	N/A	NP_001284684.2	E3W980
HELQ	NM_001297756.2		c.-112-47C>T	intron	N/A	NP_001284685.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HELQ	ENST00000295488.8	TSL:1 MANE Select	c.1393-47C>T	intron	N/A	ENSP00000295488.3	Q8TDG4-1
HELQ	ENST00000510985.1	TSL:1	c.1192-47C>T	intron	N/A	ENSP00000424539.1	E3W980
HELQ	ENST00000508591.5	TSL:1	n.1393-47C>T	intron	N/A	ENSP00000424186.1	E3W982

Frequencies

GnomAD3 genomes

AF:

0.503

AC:

76345

AN:

151682

Hom.:

19572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.460

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.570

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.667

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.497

Gnomad OTH

AF:

0.474

GnomAD2 exomes

AF:

0.539

AC:

131808

AN:

244660

AF XY:

0.536

show subpopulations

Gnomad AFR exome

AF:

0.450

Gnomad AMR exome

AF:

0.662

Gnomad ASJ exome

AF:

0.448

Gnomad EAS exome

AF:

0.667

Gnomad FIN exome

AF:

0.519

Gnomad NFE exome

AF:

0.492

Gnomad OTH exome

AF:

0.520

GnomAD4 exome

AF:

0.508

AC:

564255

AN:

1111422

Hom.:

146195

Cov.:

AF XY:

0.510

AC XY:

290537

AN XY:

569176

show subpopulations

African (AFR)

AF:

0.457

AC:

12205

AN:

26692

American (AMR)

AF:

0.650

AC:

28103

AN:

43214

Ashkenazi Jewish (ASJ)

AF:

0.446

AC:

10667

AN:

23922

East Asian (EAS)

AF:

0.641

AC:

24440

AN:

38148

South Asian (SAS)

AF:

0.593

AC:

46371

AN:

78218

European-Finnish (FIN)

AF:

0.520

AC:

26117

AN:

50262

Middle Eastern (MID)

AF:

0.467

AC:

2379

AN:

5092

European-Non Finnish (NFE)

AF:

0.488

AC:

389082

AN:

796896

Other (OTH)

AF:

0.508

AC:

24891

AN:

48978

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

13513

27026

40539

54052

67565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9868

19736

29604

39472

49340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.504

AC:

76438

AN:

151800

Hom.:

19610

Cov.:

AF XY:

0.510

AC XY:

37800

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.460

AC:

19023

AN:

41360

American (AMR)

AF:

0.570

AC:

8691

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.439

AC:

1524

AN:

3472

East Asian (EAS)

AF:

0.667

AC:

3442

AN:

5160

South Asian (SAS)

AF:

0.613

AC:

2947

AN:

4810

European-Finnish (FIN)

AF:

0.512

AC:

5385

AN:

10512

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.497

AC:

33776

AN:

67934

Other (OTH)

AF:

0.477

AC:

1006

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1924

3848

5773

7697

9621

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.504

Hom.:

3617

Bravo

AF:

0.501

Asia WGS

AF:

0.660

AC:

2290

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.96

(source)

DANN

Benign

0.42

PhyloP100

-0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over