Variant 2-7024447-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014746.6(RNF144A):c.588A>G(p.Glu196Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,612,408 control chromosomes in the GnomAD database, including 106,714 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7733 hom., cov: 33)

Exomes 𝑓: 0.36 ( 98981 hom. )

Consequence

RNF144A
NM_014746.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.325

Variant links:

Genes affected

RNF144A (HGNC:20457): (ring finger protein 144A) This gene encodes a member of a family of RING finger domain-containing E3 ubiquitin ligases that also includes parkin and parc. The expression of this gene is induced by DNA damage. The encoded protein interacts with the cytoplasmic DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) and promotes its degradation through ubiquitination. The orthologous mouse protein has been shown to interact with a ubiquitin-conjugating enzyme involved in embryonic development. [provided by RefSeq, Mar 2017]

RNF144A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 2-7024447-A-G is Benign according to our data. Variant chr2-7024447-A-G is described in ClinVar as [Benign]. Clinvar id is 1250987.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.325 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF144A	NM_014746.6 link	c.588A>G	p.Glu196Glu	synonymous_variant	7/9	ENST00000320892.11	NP_055561.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
RNF144A	ENST00000320892.11 link	c.588A>G	p.Glu196Glu	synonymous_variant	7/9	1	NM_014746.6	ENSP00000321330.6	P50876
RNF144A	ENST00000432850.1 link	c.573A>G	p.Glu191Glu	synonymous_variant	5/7	3		ENSP00000411616.1	H7C3G0
RNF144A	ENST00000467276.5 link	n.709A>G		non_coding_transcript_exon_variant	4/6	3

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45685

AN:

152074

Hom.:

7727

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.378

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.342

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.294

GnomAD3 exomes

AF:

0.349

AC:

87710

AN:

251310

Hom.:

16237

AF XY:

0.355

AC XY:

48202

AN XY:

135846

show subpopulations

Gnomad AFR exome

AF:

0.146

Gnomad AMR exome

AF:

0.401

Gnomad ASJ exome

AF:

0.405

Gnomad EAS exome

AF:

0.157

Gnomad SAS exome

AF:

0.406

Gnomad FIN exome

AF:

0.346

Gnomad NFE exome

AF:

0.373

Gnomad OTH exome

AF:

0.355

GnomAD4 exome

AF:

0.364

AC:

531206

AN:

1460216

Hom.:

98981

Cov.:

AF XY:

0.366

AC XY:

265667

AN XY:

726056

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.402

Gnomad4 ASJ exome

AF:

0.399

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.404

Gnomad4 FIN exome

AF:

0.345

Gnomad4 NFE exome

AF:

0.373

Gnomad4 OTH exome

AF:

0.353

GnomAD4 genome

AF:

0.300

AC:

45716

AN:

152192

Hom.:

7733

Cov.:

AF XY:

0.301

AC XY:

22380

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.150

Gnomad4 AMR

AF:

0.379

Gnomad4 ASJ

AF:

0.407

Gnomad4 EAS

AF:

0.162

Gnomad4 SAS

AF:

0.386

Gnomad4 FIN

AF:

0.342

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.295

Alfa

AF:

0.342

Hom.:

4824

Bravo

AF:

0.296

Asia WGS

AF:

0.262

AC:

909

AN:

3478

EpiCase

AF:

0.364

EpiControl

AF:

0.368

ClinVar

Significance: Benign

Submissions summary: Benign:2

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	GeneDx	Jan 30, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

0.81

DANN

Benign

0.34

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