chr16-71775631-C-T

Variant names:

• chr16-71775631-C-T
• rs951939
• NM_001128.6:c.202-1039G>A

Variant summary

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

The NM_001128.6(AP1G1):​c.202-1039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,858 control chromosomes in the GnomAD database, including 9,668 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 0.34 (9668 hom., cov: 31)
• Consequence: AP1G1 NM_001128.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP1G1	NM_001128.6	c.202-1039G>A		intron_variant	Intron 2 of 22	ENST00000299980.9	NP_001119.3
AP1G1	NM_001030007.2	c.202-1039G>A		intron_variant	Intron 2 of 23		NP_001025178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP1G1	ENST00000299980.9	c.202-1039G>A		intron_variant	Intron 2 of 22	1	NM_001128.6	ENSP00000299980.4

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51870 AN: 151740 Hom.: 9664 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.342 AC: 51884 AN: 151858 Hom.: 9668 Cov.: 31 AF XY: 0.347 AC XY: 25719 AN XY: 74196

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.310

Alfa AF: 0.336 Hom.: 1078

Bravo AF: 0.350

Asia WGS AF: 0.513 AC: 1781 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.70

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: rs951939; hg19: chr16-71809534;