Variant 7-101156689-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000337619.11(AP1S1):c.99C>T(p.Arg33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,609,950 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0055 ( 14 hom., cov: 32)

Exomes 𝑓: 0.0052 ( 76 hom. )

Consequence

AP1S1
ENST00000337619.11 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.313

Variant links:

Genes affected

AP1S1 (HGNC:559): (adaptor related protein complex 1 subunit sigma 1) The protein encoded by this gene is part of the clathrin coat assembly complex which links clathrin to receptors in coated vesicles. These vesicles are involved in endocytosis and Golgi processing. This protein, as well as beta-prime-adaptin, gamma-adaptin, and the medium (mu) chain AP47, form the AP-1 assembly protein complex located at the Golgi vesicle. [provided by RefSeq, Jul 2008]

AP1S1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 7-101156689-C-T is Benign according to our data. Variant chr7-101156689-C-T is described in ClinVar as [Benign]. Clinvar id is 785736.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AP1S1	NM_001283.5 linkuse as main transcript	c.99C>T	p.Arg33=	synonymous_variant	2/5	ENST00000337619.11	NP_001274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AP1S1	ENST00000337619.11 linkuse as main transcript	c.99C>T	p.Arg33=	synonymous_variant	2/5	1	NM_001283.5	ENSP00000336666	P4	P61966-1

Frequencies

GnomAD3 genomes

AF:

0.00548

AC:

833

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00176

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00924

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.0620

Gnomad SAS

AF:

0.0120

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00328

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00771

AC:

1863

AN:

241676

Hom.:

AF XY:

0.00767

AC XY:

1004

AN XY:

130954

show subpopulations

Gnomad AFR exome

AF:

0.00132

Gnomad AMR exome

AF:

0.00326

Gnomad ASJ exome

AF:

0.00122

Gnomad EAS exome

AF:

0.0598

Gnomad SAS exome

AF:

0.0110

Gnomad FIN exome

AF:

0.000189

Gnomad NFE exome

AF:

0.00280

Gnomad OTH exome

AF:

0.00607

GnomAD4 exome

AF:

0.00521

AC:

7596

AN:

1457708

Hom.:

Cov.:

AF XY:

0.00531

AC XY:

3846

AN XY:

724598

show subpopulations

Gnomad4 AFR exome

AF:

0.00123

Gnomad4 AMR exome

AF:

0.00344

Gnomad4 ASJ exome

AF:

0.000886

Gnomad4 EAS exome

AF:

0.0452

Gnomad4 SAS exome

AF:

0.0100

Gnomad4 FIN exome

AF:

0.000132

Gnomad4 NFE exome

AF:

0.00376

Gnomad4 OTH exome

AF:

0.00919

GnomAD4 genome

AF:

0.00548

AC:

834

AN:

152242

Hom.:

Cov.:

AF XY:

0.00551

AC XY:

410

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.00176

Gnomad4 AMR

AF:

0.00923

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.0624

Gnomad4 SAS

AF:

0.0120

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00328

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00349

Hom.:

Bravo

AF:

0.00652

Asia WGS

AF:

0.0530

AC:

184

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	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.38

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.38

Position offset: -6

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