rs4134932

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_004722.4(AP4M1):c.1305C>T(p.Asn435=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0286 in 1,613,992 control chromosomes in the GnomAD database, including 834 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 44 hom., cov: 32)

Exomes 𝑓: 0.030 ( 790 hom. )

Consequence

AP4M1
NM_004722.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.27

Variant links:

Genes affected

AP4M1 (HGNC:574): (adaptor related protein complex 4 subunit mu 1) This gene encodes a subunit of the heterotetrameric AP-4 complex. The encoded protein belongs to the adaptor complexes medium subunits family. This AP-4 complex is involved in the recognition and sorting of cargo proteins with tyrosine-based motifs from the trans-golgi network to the endosomal-lysosomal system. [provided by RefSeq, Jul 2008]

AP4M1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 7-100106825-C-T is Benign according to our data. Variant chr7-100106825-C-T is described in ClinVar as [Benign]. Clinvar id is 128404.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-100106825-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.27 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0184 (2800/152344) while in subpopulation NFE AF= 0.0299 (2031/68030). AF 95% confidence interval is 0.0288. There are 44 homozygotes in gnomad4. There are 1333 alleles in male gnomad4 subpopulation. This position pass quality control queck.

BS2

High Homozygotes in GnomAd at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AP4M1	NM_004722.4 linkuse as main transcript	c.1305C>T	p.Asn435=	synonymous_variant	15/15	ENST00000359593.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AP4M1	ENST00000359593.9 linkuse as main transcript	c.1305C>T	p.Asn435=	synonymous_variant	15/15	1	NM_004722.4	P3

Frequencies

GnomAD3 genomes

AF:

0.0184

AC:

2802

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00622

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.00838

Gnomad ASJ

AF:

0.0245

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0203

Gnomad FIN

AF:

0.0135

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0299

Gnomad OTH

AF:

0.0139

GnomAD3 exomes

AF:

0.0191

AC:

4794

AN:

251092

Hom.:

AF XY:

0.0204

AC XY:

2776

AN XY:

135830

show subpopulations

Gnomad AFR exome

AF:

0.00573

Gnomad AMR exome

AF:

0.00787

Gnomad ASJ exome

AF:

0.0202

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0222

Gnomad FIN exome

AF:

0.0150

Gnomad NFE exome

AF:

0.0272

Gnomad OTH exome

AF:

0.0227

GnomAD4 exome

AF:

0.0296

AC:

43296

AN:

1461648

Hom.:

790

Cov.:

AF XY:

0.0296

AC XY:

21519

AN XY:

727142

show subpopulations

Gnomad4 AFR exome

AF:

0.00484

Gnomad4 AMR exome

AF:

0.00823

Gnomad4 ASJ exome

AF:

0.0204

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0246

Gnomad4 FIN exome

AF:

0.0160

Gnomad4 NFE exome

AF:

0.0336

Gnomad4 OTH exome

AF:

0.0292

GnomAD4 genome

AF:

0.0184

AC:

2800

AN:

152344

Hom.:

Cov.:

AF XY:

0.0179

AC XY:

1333

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00620

Gnomad4 AMR

AF:

0.00837

Gnomad4 ASJ

AF:

0.0245

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0201

Gnomad4 FIN

AF:

0.0135

Gnomad4 NFE

AF:

0.0299

Gnomad4 OTH

AF:

0.0137

Alfa

AF:

0.0271

Hom.:

Bravo

AF:

0.0179

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.0308

EpiControl

AF:

0.0286

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Apr 01, 2013	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 01, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Hereditary spastic paraplegia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Nov 27, 2021

- -

Hereditary spastic paraplegia 50

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

Cadd

Benign

6.9

Dann

Benign

0.88

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