chr17-35617036-C-G

Position:

• chr17-35617036-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001030006.2(AP2B1):​c.526-7361C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,124 control chromosomes in the GnomAD database, including 3,605 homozygotes. 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 0.21 (3605 hom., cov: 31)
• Consequence: AP2B1 NM_001030006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

Genes affected

AP2B1 (HGNC:563): (adaptor related protein complex 2 subunit beta 1) The protein encoded by this gene is one of two large chain components of the assembly protein complex 2, which serves to link clathrin to receptors in coated vesicles. The encoded protein is found on the cytoplasmic face of coated vesicles in the plasma membrane. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

AP2B1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AP2B1	NM_001030006.2	c.526-7361C>G		intron_variant		ENST00000610402.5	NP_001025177.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AP2B1	ENST00000610402.5	c.526-7361C>G		intron_variant		1	NM_001030006.2	ENSP00000483185.1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32388 AN: 152006 Hom.: 3600 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.219

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.213 AC: 32426 AN: 152124 Hom.: 3605 Cov.: 31 AF XY: 0.214 AC XY: 15947 AN XY: 74382

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.223

Alfa AF: 0.191 Hom.: 1642

Bravo AF: 0.223

Asia WGS AF: 0.279 AC: 974 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.64

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

Other links and lift over

dbSNP: rs16971217; hg19: chr17-33944055;