Variant 8-144513202-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_004260.4(RECQL4):c.2463+16C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00758 in 1,534,620 control chromosomes in the GnomAD database, including 88 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0071 ( 9 hom., cov: 33)

Exomes 𝑓: 0.0076 ( 79 hom. )

Consequence

RECQL4
NM_004260.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.44

Variant links:

Genes affected

RECQL4 (HGNC:9949): (RecQ like helicase 4) The protein encoded by this gene is a DNA helicase that belongs to the RecQ helicase family. DNA helicases unwind double-stranded DNA into single-stranded DNAs and may modulate chromosome segregation. This gene is predominantly expressed in thymus and testis. Mutations in this gene are associated with Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. [provided by RefSeq, Jan 2010]

RECQL4 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 8-144513202-G-T is Benign according to our data. Variant chr8-144513202-G-T is described in ClinVar as [Benign]. Clinvar id is 445471.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-144513202-G-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00707 (1070/151316) while in subpopulation AMR AF= 0.0114 (174/15226). AF 95% confidence interval is 0.01. There are 9 homozygotes in gnomad4. There are 566 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RECQL4	NM_004260.4 linkuse as main transcript	c.2463+16C>A		intron_variant		ENST00000617875.6	NP_004251.4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
RECQL4	ENST00000617875.6 linkuse as main transcript	c.2463+16C>A	intron_variant	1	NM_004260.4	ENSP00000482313	P1
RECQL4	ENST00000621189.4 linkuse as main transcript	c.1392+16C>A	intron_variant	1		ENSP00000483145
	ENST00000580385.1 linkuse as main transcript	n.271+365G>T	intron_variant, non_coding_transcript_variant	3
RECQL4	ENST00000534626.6 linkuse as main transcript	c.635-64C>A	intron_variant	5		ENSP00000477457

Frequencies

GnomAD3 genomes

AF:

0.00708

AC:

1070

AN:

151216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00155

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0114

Gnomad ASJ

AF:

0.00348

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.000626

Gnomad FIN

AF:

0.0214

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00854

Gnomad OTH

AF:

0.00725

GnomAD3 exomes

AF:

0.0131

AC:

1477

AN:

112448

Hom.:

AF XY:

0.0131

AC XY:

787

AN XY:

60134

show subpopulations

Gnomad AFR exome

AF:

0.00241

Gnomad AMR exome

AF:

0.0125

Gnomad ASJ exome

AF:

0.00971

Gnomad EAS exome

AF:

0.00117

Gnomad SAS exome

AF:

0.00253

Gnomad FIN exome

AF:

0.0450

Gnomad NFE exome

AF:

0.0171

Gnomad OTH exome

AF:

0.0177

GnomAD4 exome

AF:

0.00763

AC:

10556

AN:

1383304

Hom.:

Cov.:

AF XY:

0.00753

AC XY:

5142

AN XY:

682504

show subpopulations

Gnomad4 AFR exome

AF:

0.00129

Gnomad4 AMR exome

AF:

0.00854

Gnomad4 ASJ exome

AF:

0.00438

Gnomad4 EAS exome

AF:

0.000239

Gnomad4 SAS exome

AF:

0.00113

Gnomad4 FIN exome

AF:

0.0237

Gnomad4 NFE exome

AF:

0.00814

Gnomad4 OTH exome

AF:

0.00666

GnomAD4 genome

AF:

0.00707

AC:

1070

AN:

151316

Hom.:

Cov.:

AF XY:

0.00766

AC XY:

566

AN XY:

73904

show subpopulations

Gnomad4 AFR

AF:

0.00154

Gnomad4 AMR

AF:

0.0114

Gnomad4 ASJ

AF:

0.00348

Gnomad4 EAS

AF:

0.000195

Gnomad4 SAS

AF:

0.000626

Gnomad4 FIN

AF:

0.0214

Gnomad4 NFE

AF:

0.00855

Gnomad4 OTH

AF:

0.00718

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Jun 15, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.064

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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