Variant 12-124948072-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000544745.2(DHX37):c.2872C>T(p.Gln958Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 1,614,202 control chromosomes in the GnomAD database, including 1,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.056 ( 314 hom., cov: 34)

Exomes 𝑓: 0.038 ( 1375 hom. )

Consequence

DHX37
ENST00000544745.2 stop_gained

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.17

Variant links:

Genes affected

DHX37 (HGNC:17210): (DEAH-box helicase 37) This gene encodes a DEAD box protein. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. [provided by RefSeq, Jul 2008]

DHX37 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-124948072-G-A is Benign according to our data. Variant chr12-124948072-G-A is described in ClinVar as [Benign]. Clinvar id is 1921907.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DHX37	NM_032656.4 linkuse as main transcript	c.3388+12C>T		intron_variant		ENST00000308736.7
DHX37	XM_005253590.4 linkuse as main transcript	c.3400C>T	p.Gln1134Ter	stop_gained	26/26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
DHX37	ENST00000544745.2 linkuse as main transcript	c.2872C>T	p.Gln958Ter	stop_gained	23/23	1
DHX37	ENST00000308736.7 linkuse as main transcript	c.3388+12C>T		intron_variant		1	NM_032656.4	P1
DHX37	ENST00000507267.2 linkuse as main transcript	n.532+12C>T		intron_variant, non_coding_transcript_variant		1
DHX37	ENST00000542400.5 linkuse as main transcript	n.2002+12C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0564

AC:

8587

AN:

152216

Hom.:

312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0991

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0499

Gnomad ASJ

AF:

0.0372

Gnomad EAS

AF:

0.0812

Gnomad SAS

AF:

0.0492

Gnomad FIN

AF:

0.0299

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0357

Gnomad OTH

AF:

0.0555

GnomAD3 exomes

AF:

0.0433

AC:

10894

AN:

251352

Hom.:

316

AF XY:

0.0429

AC XY:

5830

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.100

Gnomad AMR exome

AF:

0.0302

Gnomad ASJ exome

AF:

0.0354

Gnomad EAS exome

AF:

0.0841

Gnomad SAS exome

AF:

0.0442

Gnomad FIN exome

AF:

0.0285

Gnomad NFE exome

AF:

0.0355

Gnomad OTH exome

AF:

0.0518

GnomAD4 exome

AF:

0.0385

AC:

56260

AN:

1461868

Hom.:

1375

Cov.:

AF XY:

0.0389

AC XY:

28297

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.0323

Gnomad4 ASJ exome

AF:

0.0348

Gnomad4 EAS exome

AF:

0.0776

Gnomad4 SAS exome

AF:

0.0430

Gnomad4 FIN exome

AF:

0.0280

Gnomad4 NFE exome

AF:

0.0348

Gnomad4 OTH exome

AF:

0.0480

GnomAD4 genome

AF:

0.0565

AC:

8600

AN:

152334

Hom.:

314

Cov.:

AF XY:

0.0558

AC XY:

4157

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.0992

Gnomad4 AMR

AF:

0.0498

Gnomad4 ASJ

AF:

0.0372

Gnomad4 EAS

AF:

0.0808

Gnomad4 SAS

AF:

0.0492

Gnomad4 FIN

AF:

0.0299

Gnomad4 NFE

AF:

0.0357

Gnomad4 OTH

AF:

0.0559

Alfa

AF:

0.0402

Hom.:

276

Bravo

AF:

0.0590

TwinsUK

AF:

0.0348

AC:

129

ALSPAC

AF:

0.0358

AC:

138

ESP6500AA

AF:

0.0980

AC:

432

ESP6500EA

AF:

0.0388

AC:

334

ExAC

AF:

0.0446

AC:

5416

Asia WGS

AF:

0.0980

AC:

342

AN:

3478

EpiCase

AF:

0.0419

EpiControl

AF:

0.0407

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

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.4

DANN

Benign

0.88

Eigen

Benign

-0.57

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.15

MutationTaster

Benign

0.0021

P;P

Vest4

0.017

GERP RS

1.1

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