Genetic Variant NM_024666.5:c.452-715A>T (chr15-67232612-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_024666.5(AAGAB):c.452-715A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

AAGAB
NM_024666.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.94

Publications

10 publications found

Variant links:

Genes affected

AAGAB (HGNC:25662): (alpha and gamma adaptin binding protein) The protein encoded by this gene interacts with the gamma-adaptin and alpha-adaptin subunits of complexes involved in clathrin-coated vesicle trafficking. Mutations in this gene are associated with type I punctate palmoplantar keratoderma. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2012]

AAGAB links:

RPS24P16 (HGNC:35542): (ribosomal protein S24 pseudogene 16)

RPS24P16 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024666.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
AAGAB	NM_024666.5	MANE Select	c.452-715A>T	intron	N/A	NP_078942.3
AAGAB	NM_001271885.2		c.125-715A>T	intron	N/A	NP_001258814.1
AAGAB	NM_001271886.2		c.125-715A>T	intron	N/A	NP_001258815.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
AAGAB	ENST00000261880.10	TSL:1 MANE Select	c.452-715A>T	intron	N/A	ENSP00000261880.5
RPS24P16	ENST00000497294.1	TSL:6	n.167T>A	non_coding_transcript_exon	Exon 1 of 1
AAGAB	ENST00000542650.5	TSL:2	c.125-715A>T	intron	N/A	ENSP00000440735.1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

152034

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

229324

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

132970

African (AFR)

AF:

0.00

AC:

AN:

6076

American (AMR)

AF:

0.00

AC:

AN:

26684

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

7182

East Asian (EAS)

AF:

0.00

AC:

AN:

9416

South Asian (SAS)

AF:

0.00

AC:

AN:

39408

European-Finnish (FIN)

AF:

0.00

AC:

AN:

11140

Middle Eastern (MID)

AF:

0.00

AC:

AN:

754

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

118202

Other (OTH)

AF:

0.00

AC:

AN:

10462

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

152034

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74270

African (AFR)

AF:

0.00

AC:

AN:

41364

American (AMR)

AF:

0.00

AC:

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5196

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10574

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68010

Other (OTH)

AF:

0.00

AC:

AN:

2090

Alfa

AF:

0.00

Hom.:

2775

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

(source)

DANN

Benign

0.92

PhyloP100

2.9

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over