Variant rs610037 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000532090.3(AP5B1):c.1107T>G(p.Leu369=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,598,098 control chromosomes in the GnomAD database, including 217,303 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 0.52 ( 21108 hom., cov: 33)

Exomes 𝑓: 0.51 ( 196195 hom. )

Consequence

AP5B1
ENST00000532090.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

Variant links:

Genes affected

AP5B1 (HGNC:25104): (adaptor related protein complex 5 subunit beta 1) Involved in endosomal transport. Located in lysosomal membrane. Part of AP-type membrane coat adaptor complex. [provided by Alliance of Genome Resources, Apr 2022]

AP5B1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP7

Synonymous conserved (PhyloP=0.317 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AP5B1	NM_138368.5 linkuse as main transcript	c.1107T>G	p.Leu369=	synonymous_variant	2/2	ENST00000532090.3	NP_612377.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AP5B1	ENST00000532090.3 linkuse as main transcript	c.1107T>G	p.Leu369=	synonymous_variant	2/2	1	NM_138368.5	ENSP00000454303	P1

Frequencies

GnomAD3 genomes

AF:

0.518

AC:

78784

AN:

151992

Hom.:

21079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.434

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.355

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.531

Gnomad OTH

AF:

0.522

GnomAD3 exomes

AF:

0.454

AC:

105404

AN:

232126

Hom.:

25121

AF XY:

0.452

AC XY:

57311

AN XY:

126762

show subpopulations

Gnomad AFR exome

AF:

0.612

Gnomad AMR exome

AF:

0.345

Gnomad ASJ exome

AF:

0.427

Gnomad EAS exome

AF:

0.352

Gnomad SAS exome

AF:

0.294

Gnomad FIN exome

AF:

0.418

Gnomad NFE exome

AF:

0.535

Gnomad OTH exome

AF:

0.494

GnomAD4 exome

AF:

0.514

AC:

743709

AN:

1445986

Hom.:

196195

Cov.:

AF XY:

0.508

AC XY:

364462

AN XY:

717710

show subpopulations

Gnomad4 AFR exome

AF:

0.615

Gnomad4 AMR exome

AF:

0.353

Gnomad4 ASJ exome

AF:

0.428

Gnomad4 EAS exome

AF:

0.361

Gnomad4 SAS exome

AF:

0.297

Gnomad4 FIN exome

AF:

0.431

Gnomad4 NFE exome

AF:

0.546

Gnomad4 OTH exome

AF:

0.518

GnomAD4 genome

AF:

0.518

AC:

78857

AN:

152112

Hom.:

21108

Cov.:

AF XY:

0.505

AC XY:

37537

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.612

Gnomad4 AMR

AF:

0.434

Gnomad4 ASJ

AF:

0.430

Gnomad4 EAS

AF:

0.355

Gnomad4 SAS

AF:

0.304

Gnomad4 FIN

AF:

0.393

Gnomad4 NFE

AF:

0.531

Gnomad4 OTH

AF:

0.519

Alfa

AF:

0.517

Hom.:

32176

Bravo

AF:

0.529

Asia WGS

AF:

0.397

AC:

1381

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.81

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