Genetic Variant RNF145:c.*687G>A (chr5-159157983-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001199383.2(RNF145):c.*687G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,766 control chromosomes in the GnomAD database, including 57,341 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 0.86 ( 57185 hom., cov: 31)

Exomes 𝑓: 0.76 ( 156 hom. )

Consequence

RNF145
NM_001199383.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140

Variant links:

Genes affected

RNF145 (HGNC:20853): (ring finger protein 145) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein ubiquitination. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

RNF145 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF145	NM_001199383.2 link	c.*687G>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000424310.7	NP_001186312.1	Q96MT1-1A8K9Y9Q8NDT8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF145	ENST00000424310 link	c.*687G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_001199383.2	ENSP00000409064.2		Q96MT1-1

Frequencies

GnomAD3 genomes

AF:

0.864

AC:

131368

AN:

152098

Hom.:

57132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.961

Gnomad AMI

AF:

0.897

Gnomad AMR

AF:

0.885

Gnomad ASJ

AF:

0.806

Gnomad EAS

AF:

0.907

Gnomad SAS

AF:

0.919

Gnomad FIN

AF:

0.759

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.859

GnomAD4 exome

AF:

0.764

AC:

422

AN:

552

Hom.:

156

Cov.:

AF XY:

0.764

AC XY:

249

AN XY:

326

show subpopulations

Gnomad4 AMR exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.828

Gnomad4 FIN exome

AF:

0.740

Gnomad4 NFE exome

AF:

0.813

Gnomad4 OTH exome

AF:

0.750

GnomAD4 genome

AF:

0.864

AC:

131477

AN:

152214

Hom.:

57185

Cov.:

AF XY:

0.864

AC XY:

64267

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.961

Gnomad4 AMR

AF:

0.885

Gnomad4 ASJ

AF:

0.806

Gnomad4 EAS

AF:

0.907

Gnomad4 SAS

AF:

0.919

Gnomad4 FIN

AF:

0.759

Gnomad4 NFE

AF:

0.811

Gnomad4 OTH

AF:

0.856

Alfa

AF:

0.824

Hom.:

47235

Bravo

AF:

0.875

Asia WGS

AF:

0.902

AC:

3138

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

7.8

DANN

Benign

0.83

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over