NM_001283.5:c.3+25_3+40dupAGGGGGAAGCGAGGGG

Variant names:

• chr7-101154535-G-GGAGGGGAGGGGGAAGC
• NM_001283.5:c.3+25_3+40dupAGGGGGAAGCGAGGGG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001283.5(AP1S1):​c.3+25_3+40dupAGGGGGAAGCGAGGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: AP1S1 NM_001283.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.49

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 7-101154535-G-GGAGGGGAGGGGGAAGC is Benign according to our data. Variant chr7-101154535-G-GGAGGGGAGGGGGAAGC is described in ClinVar as [Likely_benign]. Clinvar id is 2798206.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP1S1	NM_001283.5	c.3+25_3+40dupAGGGGGAAGCGAGGGG		intron_variant	Intron 1 of 4	ENST00000337619.11	NP_001274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP1S1	ENST00000337619.11	c.3+25_3+40dupAGGGGGAAGCGAGGGG		intron_variant	Intron 1 of 4	1	NM_001283.5	ENSP00000336666.5
AP1S1	ENST00000429457.1	c.16_31dupAGGGGGAAGCGAGGGG	p.Ala11LysfsTer183	frameshift_variant	Exon 1 of 5	5		ENSP00000399902.1
AP1S1	ENST00000443943.5	n.3+25_3+40dupAGGGGGAAGCGAGGGG		intron_variant	Intron 1 of 5	3		ENSP00000410780.1
AP1S1	ENST00000646950.1	n.3+25_3+40dupAGGGGGAAGCGAGGGG		intron_variant	Intron 1 of 4			ENSP00000496332.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 03, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-100797816;