rs3760318

chr17-30920697-G-A

Variant summary

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

The ENST00000583688.1(ADAP2):n.302-1007G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,004 control chromosomes in the GnomAD database, including 11,629 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 0.39 (11629 hom., cov: 32)
• Consequence: ADAP2 ENST00000583688.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

Genes affected

ADAP2 (HGNC:16487): (ArfGAP with dual PH domains 2) The protein encoded by this gene binds beta-tubulin and increases the stability of microtubules. The encoded protein can also translocate to the cell membrane and bind phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). In addition, this protein is a GTPase-activating protein for ADP ribosylation factor 6 and may be able to block the entry of some RNA viruses. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAP2	ENST00000583688.1	n.302-1007G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59127 AN: 151886 Hom.: 11604 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.390 AC: 59212 AN: 152004 Hom.: 11629 Cov.: 32 AF XY: 0.388 AC XY: 28808 AN XY: 74276

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.370

Alfa AF: 0.377 Hom.: 24844

Bravo AF: 0.391

Asia WGS AF: 0.330 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.36
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760318; hg19: chr17-29247715;