Variant rs3744028 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_173547.4(TRIM65):c.511-91A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,322,824 control chromosomes in the GnomAD database, including 29,428 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 0.26 ( 6678 hom., cov: 33)

Exomes 𝑓: 0.19 ( 22750 hom. )

Consequence

TRIM65
NM_173547.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.698

Variant links:

Genes affected

TRIM65 (HGNC:27316): (tripartite motif containing 65) Predicted to enable zinc ion binding activity. Involved in positive regulation of autophagy. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TRIM65 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM65	NM_173547.4 linkuse as main transcript	c.511-91A>G		intron_variant		ENST00000269383.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM65	ENST00000269383.8 linkuse as main transcript	c.511-91A>G		intron_variant		1	NM_173547.4	P1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39914

AN:

151996

Hom.:

6652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.188

AC:

219614

AN:

1170710

Hom.:

22750

Cov.:

AF XY:

0.188

AC XY:

109532

AN XY:

583020

show subpopulations

Gnomad4 AFR exome

AF:

0.488

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.198

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.187

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.183

Gnomad4 OTH exome

AF:

0.208

GnomAD4 genome

AF:

0.263

AC:

39995

AN:

152114

Hom.:

6678

Cov.:

AF XY:

0.257

AC XY:

19129

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.474

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.203

Gnomad4 EAS

AF:

0.132

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.109

Gnomad4 NFE

AF:

0.191

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.225

Hom.:

569

Bravo

AF:

0.280

Asia WGS

AF:

0.193

AC:

671

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.0

DANN

Benign

0.35

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over