Variant chr2-38802766-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_198963.3(DHX57):c.3966C>T(p.Phe1322Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00283 in 1,614,100 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0029 ( 17 hom. )

Consequence

DHX57
NM_198963.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.117

Variant links:

Genes affected

DHX57 (HGNC:20086): (DExH-box helicase 57) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

DHX57 links:

DHX57 (HGNC:):

DHX57 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 2-38802766-G-A is Benign according to our data. Variant chr2-38802766-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650842.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.117 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DHX57	NM_198963.3 linkuse as main transcript	c.3966C>T	p.Phe1322Phe	synonymous_variant	23/24	ENST00000457308.6	NP_945314.1	Q6P158-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DHX57	ENST00000457308.6 linkuse as main transcript	c.3966C>T	p.Phe1322Phe	synonymous_variant	23/24	1	NM_198963.3	ENSP00000405111.2		Q6P158-1

Frequencies

GnomAD3 genomes

AF:

0.00216

AC:

328

AN:

152104

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0116

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00318

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00272

AC:

684

AN:

251458

Hom.:

AF XY:

0.00310

AC XY:

421

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.000983

Gnomad ASJ exome

AF:

0.000794

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00950

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.00283

Gnomad OTH exome

AF:

0.00407

GnomAD4 exome

AF:

0.00291

AC:

4248

AN:

1461878

Hom.:

Cov.:

AF XY:

0.00324

AC XY:

2357

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.000984

Gnomad4 ASJ exome

AF:

0.000459

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00982

Gnomad4 FIN exome

AF:

0.000112

Gnomad4 NFE exome

AF:

0.00279

Gnomad4 OTH exome

AF:

0.00301

GnomAD4 genome

AF:

0.00215

AC:

327

AN:

152222

Hom.:

Cov.:

AF XY:

0.00200

AC XY:

149

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.000529

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0114

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00318

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00200

Hom.:

Bravo

AF:

0.00179

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.00365

EpiControl

AF:

0.00391

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

DHX57: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

2.9

DANN

Benign

0.55

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

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