Variant 16-71734597-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000299980.9(AP1G1):c.2367+12A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 1,587,548 control chromosomes in the GnomAD database, including 111,623 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 9932 hom., cov: 32)

Exomes 𝑓: 0.37 ( 101691 hom. )

Consequence

AP1G1
ENST00000299980.9 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0190

Variant links:

Genes affected

AP1G1 (HGNC:555): (adaptor related protein complex 1 subunit gamma 1) Adaptins are important components of clathrin-coated vesicles transporting ligand-receptor complexes from the plasma membrane or from the trans-Golgi network to lysosomes. The adaptin family of proteins is composed of four classes of molecules named alpha, beta-, beta prime- and gamma- adaptins. Adaptins, together with medium and small subunits, form a heterotetrameric complex called an adaptor, whose role is to promote the formation of clathrin-coated pits and vesicles. The protein encoded by this gene is a gamma-adaptin protein and it belongs to the adaptor complexes large subunits family. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

AP1G1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 16-71734597-T-C is Benign according to our data. Variant chr16-71734597-T-C is described in ClinVar as [Benign]. Clinvar id is 1343913.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AP1G1	NM_001128.6 linkuse as main transcript	c.2367+12A>G		intron_variant		ENST00000299980.9	NP_001119.3
AP1G1	NM_001030007.2 linkuse as main transcript	c.2376+12A>G		intron_variant			NP_001025178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AP1G1	ENST00000299980.9 linkuse as main transcript	c.2367+12A>G		intron_variant		1	NM_001128.6	ENSP00000299980	P4	O43747-1

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52721

AN:

151948

Hom.:

9930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.759

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.335

Gnomad OTH

AF:

0.316

GnomAD3 exomes

AF:

0.402

AC:

100951

AN:

251052

Hom.:

23012

AF XY:

0.391

AC XY:

53064

AN XY:

135688

show subpopulations

Gnomad AFR exome

AF:

0.278

Gnomad AMR exome

AF:

0.577

Gnomad ASJ exome

AF:

0.346

Gnomad EAS exome

AF:

0.762

Gnomad SAS exome

AF:

0.343

Gnomad FIN exome

AF:

0.373

Gnomad NFE exome

AF:

0.337

Gnomad OTH exome

AF:

0.365

GnomAD4 exome

AF:

0.367

AC:

526108

AN:

1435482

Hom.:

101691

Cov.:

AF XY:

0.364

AC XY:

260848

AN XY:

715764

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.558

Gnomad4 ASJ exome

AF:

0.344

Gnomad4 EAS exome

AF:

0.701

Gnomad4 SAS exome

AF:

0.341

Gnomad4 FIN exome

AF:

0.372

Gnomad4 NFE exome

AF:

0.352

Gnomad4 OTH exome

AF:

0.371

GnomAD4 genome

AF:

0.347

AC:

52733

AN:

152066

Hom.:

9932

Cov.:

AF XY:

0.351

AC XY:

26119

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.278

Gnomad4 AMR

AF:

0.447

Gnomad4 ASJ

AF:

0.332

Gnomad4 EAS

AF:

0.758

Gnomad4 SAS

AF:

0.342

Gnomad4 FIN

AF:

0.365

Gnomad4 NFE

AF:

0.335

Gnomad4 OTH

AF:

0.314

Alfa

AF:

0.338

Hom.:

1942

Bravo

AF:

0.355

Asia WGS

AF:

0.516

AC:

1794

AN:

3478

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	Mar 13, 2022	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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