rs3760318

Variant names:

• chr17-30920697-G-A
• rs3760318
• ENST00000583688.1:n.302-1007G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-30920697-G-A
• chr17-30920697-G-C
• chr17-30920697-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000583688.1(ADAP2):​n.302-1007G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 63 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583688.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAP2	ENST00000583688.1	TSL:4	n.302-1007G>A		intron	N/A

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

African (AFR) AF: 0.443 AC: 18387 AN: 41470

American (AMR) AF: 0.381 AC: 5815 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1108 AN: 3464

East Asian (EAS) AF: 0.223 AC: 1156 AN: 5178

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3893 AN: 10534

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25669 AN: 67946

Other (OTH) AF: 0.370 AC: 782 AN: 2112

Alfa AF: 0.377 Hom.: 52411

Bravo AF: 0.391

Asia WGS AF: 0.330 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.23
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs3760318; hg19: chr17-29247715;